--- /dev/null
+This folder contains the "evoruby" Ruby classes.
+They are not (yet) essential for the rest of the FORESTER package.
+
+To use evoruby, add "path/to/forester-atv/ruby/evoruby" to RUBYLIB.
+(e.g., for C shell: "setenv RUBYLIB $HOME/forester-atv/ruby/evoruby:$HOME/some/other/rubylibrary")
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/d2f
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: d2f.rb,v 1.3 2008/08/28 17:09:06 cmzmasek Exp $
+#
+# last modified: 06/11/2007
+
+require 'lib/evo/apps/domains_to_forester'
+
+module Evoruby
+
+ dtf = DomainsToForester.new()
+
+ dtf.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/dsx
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: dsx.rb,v 1.3 2008/08/28 17:09:06 cmzmasek Exp $
+#
+# last modified: 06/11/2007
+
+require 'lib/evo/apps/domain_sequence_extractor'
+
+module Evoruby
+
+ dsx = DomainSequenceExtractor.new()
+
+ dsx.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -W0
+#
+# = exe/evo_nursery
+#
+# Copyright:: Copyright (C) 2009-2010 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: evo_nursery.rb,v 1.1 2009/10/07 21:59:41 cmzmasek Exp $
+#
+# last modified: 2009/10/07
+
+require 'lib/evo/apps/evo_nursery'
+
+module Evoruby
+
+ en = EvoNursery.new()
+
+ en.run()
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/fae
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fae.rb,v 1.1 2008/09/10 02:16:34 cmzmasek Exp $
+
+
+require 'lib/evo/apps/fasta_extractor'
+
+module Evoruby
+
+ mse = FastaExtractor.new()
+
+ mse.run()
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/fasta_tap
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fasta_tap.rb,v 1.1 2009/01/20 20:44:54 cmzmasek Exp $
+
+
+require 'lib/evo/apps/fasta_taxonomy_processor'
+
+module Evoruby
+
+ tap = FastaTaxonomyProcessor.new()
+
+ tap.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/hsp
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: hsp.rb,v 1.1 2009/11/25 05:42:04 cmzmasek Exp $
+#
+# last modified: 11/24/2009
+
+require 'lib/evo/apps/hmmscan_parser'
+
+module Evoruby
+
+ hsp = HmmscanParser.new()
+
+ hsp.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/msa_pro
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_pro.rb,v 1.4 2008/08/28 17:09:06 cmzmasek Exp $
+#
+
+
+require 'lib/evo/apps/msa_processor'
+
+module Evoruby
+
+ mp = MsaProcessor.new()
+
+ mp.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/d2f
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: mse.rb,v 1.2 2008/08/28 17:09:06 cmzmasek Exp $
+
+
+require 'lib/evo/apps/multi_sequence_extractor'
+
+module Evoruby
+
+ mse = MultiSequenceExtractor.new()
+
+ mse.run()
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/phylogeny_factory
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: phylogenies_decorator.rb,v 1.3 2008/08/28 17:09:06 cmzmasek Exp $
+#
+
+
+require 'lib/evo/apps/phylogenies_decorator'
+
+module Evoruby
+
+ fd = PhylogeniesDecorator.new
+
+ fd.run
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/phylogeny_factory
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: phylogeny_factory.rb,v 1.5 2008/08/28 17:09:06 cmzmasek Exp $
+#
+
+
+require 'lib/evo/apps/phylogeny_factory'
+
+module Evoruby
+
+ pf = PhylogenyFactory.new
+
+ pf.run
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = run_phylo_pipeline
+#
+# Copyright:: Copyright (C) 2010 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: run_phylo_pipeline.rb,v 1.15 2010/10/09 02:35:42 cmzmasek Exp $
+#
+#
+
+
+# hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm <BACTH_CHIPI>.fasta
+
+# hsp <BACTH_CHIPI>_hmmscan_240_10 <BACTH_CHIPI>_hmmscan_240_10_domain_table
+
+# d2f -e=10 <BACTH_CHIPI>_hmmscan_240_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_240_10.dff
+
+# hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD <~/DATA/PFAM/PFAM240/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
+
+# dsx -dd -e=<1e-2> -l=<200> <BACTH_CHIPI>.hmmsearch_SusD <BACTH_CHIPI>.fasta BACTH_CHIPI_e2_200
+
+
+module Evoruby
+
+ class RunPhyloPipeline
+
+ def run
+ unless ARGV.length == 4
+ puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]"
+ exit
+ end
+
+ hmmscan = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmscan"
+ hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmsearch"
+ hsp = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/hsp.rb"
+ d2f = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/d2f.rb"
+ dsx = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/dsx.rb"
+
+ base_name = ARGV[ 0 ]
+ hmm = ARGV[ 1 ]
+ length = ARGV[ 2 ]
+ e_value_exp = ARGV[ 3 ]
+ do_domain_combination_analysis = true
+
+ if do_domain_combination_analysis
+
+ cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm #{base_name}.fasta"
+ run_command( cmd )
+
+ cmd = "#{hsp} #{base_name}_hmmscan_240_10 #{base_name}_hmmscan_240_10_domain_table"
+ run_command( cmd )
+
+ cmd = "#{d2f} -e=10 #{base_name}_hmmscan_240_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_240_10.dff"
+ run_command( cmd )
+
+ end
+
+ cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM240/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
+ run_command( cmd )
+
+ cmd = "#{dsx} -dd -e=1e-#{e_value_exp.to_s} -l=#{length} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_e#{e_value_exp.to_s}_#{length}"
+ run_command( cmd )
+
+ end
+
+ def run_command( cmd )
+ puts cmd
+ `#{cmd}`
+ end
+
+ end
+
+ p = RunPhyloPipeline.new()
+
+ p.run()
+
+end
+
+
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/tap
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: tap.rb,v 1.3 2008/08/28 17:09:06 cmzmasek Exp $
+#
+# last modified: 05/18/2007
+
+require 'lib/evo/apps/taxonomy_processor'
+
+module Evoruby
+
+ tap = TaxonomyProcessor.new()
+
+ tap.run()
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/test - Test class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: test.rb,v 1.18 2010/10/08 22:04:17 cmzmasek Exp $
+#
+# last modified: 05/15/2007
+
+
+require 'lib/evo/util/constants'
+require 'lib/evo/taxonomy/taxonomy'
+require 'lib/evo/sequence/sequence'
+require 'lib/evo/msa/msa'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/sequence/domain_structure'
+require 'lib/evo/sequence/protein_domain'
+require 'lib/evo/table/basic_table'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/io/writer/nexus_writer'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/parser/ncbi_tseq_parser'
+require 'lib/evo/io/parser/hmmsearch_domain_extractor'
+require 'lib/evo/apps/domain_sequence_extractor'
+require 'lib/evo/apps/hmmscan_parser'
+require 'lib/evo/apps/domains_to_forester'
+require 'lib/evo/io/parser/general_msa_parser'
+require 'lib/evo/io/parser/basic_table_parser'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/soft/fastme'
+require 'lib/evo/soft/tree_puzzle'
+
+
+
+module Evoruby
+
+ class Test
+
+ GENERAL_MSA_FILE = "files/test/general_msa_file.txt"
+ FASTA_FILE = "files/test/fasta_file.txt"
+ TSEQ_FILE = "files/test/ncbi_tseq.xml"
+
+ def initialize()
+ @failures = 0
+ @successes = 0
+ end
+
+
+
+ def test_taxonomy()
+ begin
+ tax = Taxonomy.new( "pig" )
+
+ if tax.get_name != "pig"
+ return false
+ end
+
+ tax1 = Taxonomy.new( "dog", "id", "source" )
+ tax2 = tax1.copy
+
+ if tax2.get_name != "dog"
+ return false
+ end
+ if tax2.get_id != "id"
+ return false
+ end
+ if tax2.get_id_source != "source"
+ return false
+ end
+
+ if !( tax1 == tax2 )
+ return false
+ end
+
+ if !( tax1 == tax1 )
+ return false
+ end
+
+ tax3 = Taxonomy.new( "dog", "id" )
+ if ( tax1 == tax3 )
+ return false
+ end
+
+ tax4 = Taxonomy.new( "dog" )
+ tax5 = Taxonomy.new( "dog" )
+ if !( tax4 == tax5 )
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+
+ def test_sequence()
+ begin
+ seq = Sequence.new( "seq1", "WLIQ" )
+ if ( seq.get_length != 4 )
+ return false
+ end
+ if ( seq.get_residue( 3 ) != "Q" )
+ return false
+ end
+ seq.append!( "E?-*X_Y" )
+ if ( seq.get_length != 11 )
+ return false
+ end
+ if ( seq.get_residue( 3 ) != "Q" )
+ return false
+ end
+ if ( seq.get_residue( 4 ) != "E" )
+ return false
+ end
+ seq.append!( "A V_" )
+ if ( seq.get_length != 15 )
+ return false
+ end
+ if ( !Test::same?( seq.get_gap_length, 5 ) )
+ return false
+ end
+ if ( !Test::same?( seq.get_gap_ratio, 5.0 / 15.0 ) )
+ return false
+ end
+ seq.delete_residue!( 0 )
+ seq.delete_residue!( 2 )
+ seq2 = seq.copy()
+ seq.delete_residue!( 0 )
+ seq.delete_residue!( 0 )
+ seq = nil
+ if ( seq2.get_length != 13 )
+ return false
+ end
+ if ( seq2.get_sequence_as_string != "LIE?-*X_YA V_" )
+ return false
+ end
+ if ( seq2.get_slice( 2, 2 ) != "E?" )
+ return false
+ end
+ if ( seq2.get_slice( 0, 1 ) != "L" )
+ return false
+ end
+ if ( seq2.get_subsequence( 1, 4 ).get_sequence_as_string != "IE?-" )
+ return false
+ end
+ if ( seq2.get_name() != "seq1" )
+ return false
+ end
+ if ( seq2.get_slice!( 2, 2 ) != "E?" )
+ return false
+ end
+ if ( seq2.get_sequence_as_string != "LI-*X_YA V_" )
+ return false
+ end
+ if ( seq2.get_length != 11 )
+ return false
+ end
+ if ( seq2.get_character_code( 0 ) != 76 )
+ return false
+ end
+ str_0 = " Li-*X_YA V_ 3 3 1212 ?? B1J OU.Z "
+ if ( Util.clean_seq_str( str_0 ) != "LI-X-YAV-XXXXXX-X" )
+ return false
+ end
+
+ tax = Taxonomy.new( "dog", "tax_id", "tax_source" )
+ seqn = Sequence.new( "seqn", "VVVVV", "acc", "acc source", tax, "symbol", "2accession", "2source" )
+ seqc = seqn.copy
+ if ( seqc.get_name() != "seqn" )
+ return false
+ end
+ if ( seqc.get_accession() != "acc" )
+ return false
+ end
+ if ( seqc.get_accession_source() != "acc source" )
+ return false
+ end
+ if ( seqc.get_taxonomy.get_name != "dog" )
+ return false
+ end
+ if ( seqc.get_taxonomy.get_id != "tax_id" )
+ return false
+ end
+ if ( seqc.get_symbol != "symbol" )
+ return false
+ end
+ if ( seqc.get_secondary_accession != "2accession" )
+ return false
+ end
+ if ( seqc.get_secondary_accession_source != "2source" )
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+
+ def test_msa()
+ begin
+ msa = Msa.new()
+ seq0 = Sequence.new( "seq 0", "a-*-_ x-ijklmnopqrstuvwxyz" )
+ seq1 = Sequence.new( "seq 1", "ab--_ X-ijklmnopqrstuvwxyz" )
+ seq2 = Sequence.new( "seq 2", "abc-_?x-ijklmnopqrstuvwxyz" )
+ seq3 = Sequence.new( "seq 3", "abcd_?x-ijklmnopqrstuvwxyz" )
+ seq4 = Sequence.new( "seq 4", "abcde?x-ijklmnopqrstuvwxyz" )
+ seq5 = Sequence.new( "seq 5", "abcdefx-ijklmnopqrstuvwxyz" )
+ msa.add_sequence( seq0 );
+ msa.add_sequence( seq1 );
+ msa.add_sequence( seq2 );
+ msa.add_sequence( seq3 );
+ msa.add_sequence( seq4 );
+ msa.add_sequence( seq5 );
+ msa.add( "seq 6", "abcdefg-ijklmnopqrstuvwxyz" );
+ if ( msa.get_sequence( 0 ).get_name() != "seq 0" )
+ return false
+ end
+ if ( msa.get_by_name( "Eq 1", false, true ).get_name != "seq 1" )
+ return false
+ end
+ if ( msa.find_by_name( "Eq 2", false, true )[ 0 ] != 2 )
+ return false
+ end
+ if ( !msa.is_aligned )
+ return false
+ end
+ if ( msa.get_number_of_seqs != 7 )
+ return false
+ end
+ if ( msa.get_length != 26 )
+ return false
+ end
+ msa.add( "seq 7", "abcdefgqijklmnopqrstuvwxyz" );
+ if ( msa.get_number_of_seqs != 8 )
+ return false
+ end
+ msa.remove_sequence!( 7 )
+ if ( msa.get_number_of_seqs != 7 )
+ return false
+ end
+ msa.remove_gap_only_columns!()
+ if ( msa.get_length() != 25 )
+ return false
+ end
+ if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
+ return false
+ end
+ msa.remove_gap_columns_w_gap_ratio!( 6.1 / 7.0 )
+ if ( msa.get_length() != 25 )
+ return false
+ end
+ msa.remove_gap_columns_w_gap_ratio!( 6.0 / 7.0 )
+ if ( msa.get_length() != 25 )
+ return false
+ end
+ if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
+ return false
+ end
+ msa.remove_gap_columns_w_gap_ratio!( 5.0 / 7.0 )
+ if ( msa.get_length() != 25 )
+ return false
+ end
+ if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
+ return false
+ end
+ msa.remove_gap_columns_w_gap_ratio!( 2.0 / 7.0 )
+ if ( msa.get_length() != 23 )
+ return false
+ end
+ if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-* xijklmnopqrstuvwxyz" )
+ puts msa.get_by_name( "seq 0" ).get_sequence_as_string
+ return false
+ end
+ msa.remove_gap_columns_w_gap_ratio!( 1.0 / 7.0 )
+ if ( msa.get_length() != 21 )
+ return false
+ end
+ if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-xijklmnopqrstuvwxyz" )
+ return false
+ end
+ msa2 = Evoruby::Msa.new()
+ msa2.add( "seq0", "abcdefgh" );
+ msa2.add( "seq1", "a-cdefgh" );
+ msa2.add( "seq2", "a--defgh" );
+ msa2.add( "seq3", "a---efgh" );
+ msa2.add( "seq4", "a----fgh" );
+ msa2.add( "seq5", "a" );
+ if ( msa2.is_aligned )
+ return false
+ end
+ msa2.remove_sequence!( 5 )
+ if ( !msa2.is_aligned )
+ return false
+ end
+ if ( msa2.get_number_of_seqs != 5 )
+ return false
+ end
+ msa2.remove_gap_only_columns!()
+
+ if ( msa2.get_length != 8 )
+ return false
+ end
+
+ msa2.remove_sequences_by_gap_ratio!( 4.0 / 8.0 )
+ if ( msa2.get_number_of_seqs != 5 )
+ return false
+ end
+ msa2.remove_sequences_by_gap_ratio!( 3.0 / 8.0 )
+ if ( msa2.get_number_of_seqs != 4 )
+ return false
+ end
+ msa2.remove_sequences_by_gap_ratio!( 1.0 / 8.0 )
+ if ( msa2.get_number_of_seqs != 2 )
+ return false
+ end
+ msa2.remove_sequences_by_gap_ratio!( 0.0 )
+ if ( msa2.get_number_of_seqs != 1 )
+ return false
+ end
+ msa2.add( "seq1", "a-cdefgh" );
+ msa2.add( "seq2", "a--defgh" );
+ msa2.add( "seq3", "a---efgh" );
+ msa2.add( "seq4", "a----fgh" );
+
+ msa2.remove_sequences_by_non_gap_length!( 4 )
+ if ( msa2.get_number_of_seqs != 5 )
+ return false
+ end
+ msa2.remove_sequences_by_non_gap_length!( 5 )
+ if ( msa2.get_number_of_seqs != 4 )
+ return false
+ end
+ msa2.remove_sequences_by_non_gap_length!( 8 )
+ if ( msa2.get_number_of_seqs != 1 )
+ return false
+ end
+ msa2.add( "seq1", "a-cdefgh" );
+ msa2.add( "seq2", "a--defgh" );
+ msa2.add( "seq3", "a---efgh" );
+ msa2.add( "seq4", "a----fgh" );
+ msa2.trim!( 0, 7 )
+ if ( msa2.get_by_name( "seq0" ).get_sequence_as_string != "abcdefgh" )
+ return false
+ end
+ msa2.trim!( 3, 4 )
+ if ( msa2.get_by_name( "seq0" ).get_sequence_as_string != "de" )
+ return false
+ end
+ msa3 = Evoruby::Msa.new()
+ msa3.add( "seq0", "abcdefgh-abcdef--*" );
+ msa3.add( "seq1", "b-deefgh-a____f--*" );
+ msa3.add( "seq2", "A________abcdef--*" );
+ msa3.add( "seq3", "A Efgh---------*" );
+ msa3.add( "seq4", " eFhh---------*" );
+ msa3.add( "seq5", "----------------ee" );
+ if ( !Test::same?( msa3.calculate_overlap( 0, 0 ), 14 ) )
+ return false
+ end
+ if ( !Test::same?( msa3.calculate_overlap( 0, 1 ), 9 ) )
+ return false
+ end
+ if ( !Test::same?( msa3.calculate_overlap( 0, 5 ), 0 ) )
+ return false
+ end
+ if ( !Test::same?( msa3.calculate_overlap( 4, 5 ), 0 ) )
+ return false
+ end
+ if ( !msa3.overlap?( 2, 3 ) )
+ return false
+ end
+ if ( msa3.overlap?( 2, 3, 2 ) )
+ return false
+ end
+ if ( msa3.overlap?( 4, 5 ) )
+ return false
+ end
+ if ( !Test::same?( msa3.calculate_identities( 4, 5 ), 0 ) )
+ return false
+ end
+ if ( !Test::same?( msa3.calculate_identities( 3, 4 ), 3 ) )
+ return false
+ end
+ if ( msa3.split_into_overlapping_msa.length != 3 )
+ return false
+ end
+ if ( msa3.split_into_overlapping_msa( 5 ).length != 4 )
+ return false
+ end
+
+
+ msa4 = Msa.new()
+ seq0 = Sequence.new( "seq 0", "ABCDED" )
+ seq1 = Sequence.new( "seq 1", "ABCDEE" )
+ seq2 = Sequence.new( "seq 2", "abcded" )
+ seq3 = Sequence.new( "seq 3", " ABCDEE" )
+ seq4 = Sequence.new( "seq 4", "ABCDEV" )
+ seq5 = Sequence.new( "seq 5", "ABCDED" )
+ seq6 = Sequence.new( "seq 6", "AB.DEI" )
+ seq7 = Sequence.new( "seq 7", "aB-DEi*" )
+ seq8 = Sequence.new( "seq 8", "ABCDED" )
+ seq9 = Sequence.new( "seq 9", "ABCDED" )
+ seq10 = Sequence.new( "seq 10", "ABCDED" )
+ seq11 = Sequence.new( "seq 11", "ABCDED" )
+ msa4.add_sequence( seq0 );
+ msa4.add_sequence( seq1 );
+ msa4.add_sequence( seq2 );
+ msa4.add_sequence( seq3 );
+ msa4.add_sequence( seq4 );
+ msa4.add_sequence( seq5 );
+ msa4.add_sequence( seq6 );
+ msa4.add_sequence( seq7 );
+ msa4.add_sequence( seq8 );
+ msa4.add_sequence( seq9 );
+ msa4.add_sequence( seq10 );
+ msa4.add_sequence( seq11 );
+
+ msa4.remove_redundant_sequences!
+
+ puts msa4.to_str
+
+ if msa4.get_number_of_seqs != 4
+ return false
+ end
+
+ if msa4.get_sequence( 0 ).get_name != "seq 0"
+ return false
+ end
+ if msa4.get_sequence( 1 ).get_name != "seq 1"
+ return false
+ end
+ if msa4.get_sequence( 2 ).get_name != "seq 4"
+ return false
+ end
+ if msa4.get_sequence( 3 ).get_name != "seq 6"
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_msa_factory()
+ begin
+ f = MsaFactory.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_domain_structure()
+ begin
+ ds = DomainStructure.new( 190 )
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_protein_domain()
+ begin
+ ds = ProteinDomain.new( "domain", 23, 466, "d1", 0.4 )
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_basic_table()
+ begin
+ t = BasicTable.new()
+ t.set_value( 233, 923, "snake" )
+ t.set_value( 233, 923, "lizard" )
+ if ( t.get_value_as_string( 233, 923 ) != "lizard" )
+ return false
+ end
+ if ( t.get_value_as_string( 33, 23 ) != "" )
+ return false
+ end
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_msa_io()
+ begin
+ msaio = MsaIO.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_phylip_sequentialwriter()
+ begin
+ p = PhylipSequentialWriter.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_nexus_writer()
+ begin
+ n = NexusWriter.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_fasta_writer()
+ begin
+ f = FastaWriter.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_general_msa_parser( path_to_evoruby )
+ begin
+ g = GeneralMsaParser.new()
+ f = MsaFactory.new()
+ sep = ""
+ if ( !Util::is_string_empty?( path_to_evoruby ) )
+ sep = Constants::FILE_SEPARATOR
+ end
+ msa = f.create_msa_from_file( path_to_evoruby +
+ sep +
+ GENERAL_MSA_FILE, g )
+
+ if ( msa.get_length() != 29 )
+ return false
+ end
+ if ( msa.get_number_of_seqs() != 7 )
+ return false
+ end
+
+ seq0 = msa.get_sequence( 0 )
+ seq1 = msa.get_sequence( 1 )
+ seq2 = msa.get_sequence( 2 )
+ seq3 = msa.get_sequence( 3 )
+ seq4 = msa.get_sequence( 4 )
+ seq5 = msa.get_sequence( 5 )
+ seq6 = msa.get_sequence( 6 )
+
+ if ( seq0.get_name() != "sequence0" )
+ return false
+ end
+ if ( seq0.get_sequence_as_string() != "ABCDE.GHIJKLMNOPQR.TUVWabcxy0" )
+ return false
+ end
+
+ if ( seq1.get_name() != "sequence1" )
+ return false
+ end
+ if ( seq1.get_sequence_as_string() != "abcdefghijklmnopqrstuvwabcxy1" )
+ return false
+ end
+
+ if ( seq2.get_name() != "sequence2" )
+ return false
+ end
+ if ( seq2.get_sequence_as_string() != "abcdefghijkl---x_-*?_XXabcxy2" )
+ return false
+ end
+
+ if ( seq3.get_name() != "sequence3" )
+ return false
+ end
+ if ( seq3.get_sequence_as_string() != "12345678901234567890123abcxy3" )
+ return false
+ end
+
+ if ( seq4.get_name() != "sequence4" )
+ return false
+ end
+ if ( seq4.get_sequence_as_string() != "--------------------------xy4" )
+ return false
+ end
+
+ if ( seq5.get_name() != "sequence5" )
+ return false
+ end
+ if ( seq5.get_sequence_as_string() != "a*c*ef****************wabcxy5" )
+ return false
+ end
+
+ if ( seq6.get_name() != "sequence6" )
+ return false
+ end
+ if ( seq6.get_sequence_as_string() != "ururufhfghfgftgfhftgfttabcxy6" )
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_fasta_parser( path_to_evoruby )
+ begin
+ fasta = FastaParser.new()
+ f = MsaFactory.new()
+ sep = ""
+ if ( !Util::is_string_empty?( path_to_evoruby ) )
+ sep = Constants::FILE_SEPARATOR
+ end
+ msa = f.create_msa_from_file( path_to_evoruby +
+ sep +
+ FASTA_FILE, fasta )
+
+ if ( msa.get_length() != 6 )
+ return false
+ end
+ if ( msa.get_number_of_seqs() != 4 )
+ return false
+ end
+
+ seq0 = msa.get_sequence( 0 )
+ seq1 = msa.get_sequence( 1 )
+ seq2 = msa.get_sequence( 2 )
+ seq3 = msa.get_sequence( 3 )
+
+ if ( seq0.get_name() != "sequence 0" )
+ return false
+ end
+ if ( seq0.get_sequence_as_string() != "ABCDEF" )
+ return false
+ end
+
+ if ( seq1.get_name() != "sequence 1" )
+ return false
+ end
+ if ( seq1.get_sequence_as_string() != "abcdef" )
+ return false
+ end
+
+ if ( seq2.get_name() != "sequence 2" )
+ return false
+ end
+ if ( seq2.get_sequence_as_string() != "123456" )
+ return false
+ end
+ if ( seq3.get_name() != "sequence 3" )
+ return false
+ end
+ if ( seq3.get_sequence_as_string() != "a-c--f" )
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_ncbi_tseq_parser( path_to_evoruby )
+ begin
+ parser = NcbiTSeqParser.new
+ f = MsaFactory.new
+ sep = ""
+ if ( !Util::is_string_empty?( path_to_evoruby ) )
+ sep = Constants::FILE_SEPARATOR
+ end
+ msa = f.create_msa_from_file( path_to_evoruby +
+ sep +
+ TSEQ_FILE, parser )
+
+ if ( msa.get_number_of_seqs() != 9 )
+ return false
+ end
+
+ seq0 = msa.get_sequence( 0 )
+ seq1 = msa.get_sequence( 1 )
+ seq8 = msa.get_sequence( 8 )
+
+ if ( seq0.get_name() != "SusD [Bacteroides thetaiotaomicron VPI-5482]" )
+ return false
+ end
+ if ( seq0.get_sequence_as_string() != "MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK" )
+ return false
+ end
+ if ( seq0.get_accession != "29341016" )
+ return false
+ end
+ if ( seq0.get_accession_source != "gi" )
+ return false
+ end
+ if ( seq0.get_taxonomy.get_name != "Bacteroides thetaiotaomicron VPI-5482" )
+ return false
+ end
+ if ( seq0.get_taxonomy.get_id != "226186" )
+ return false
+ end
+ if ( seq0.get_taxonomy.get_id_source != "ncbi" )
+ return false
+ end
+
+
+ if ( seq1.get_name() != "SusD, outer membrane protein [Bacteroides thetaiotaomicron VPI-5482]" )
+ return false
+ end
+ if ( seq1.get_accession != "29349109" )
+ return false
+ end
+ if ( seq1.get_accession_source != "gi" )
+ return false
+ end
+ if ( seq1.get_taxonomy.get_name != "Bacteroides thetaiotaomicron VPI-5482" )
+ return false
+ end
+ if ( seq1.get_taxonomy.get_id != "226186" )
+ return false
+ end
+ if ( seq1.get_taxonomy.get_id_source != "ncbi" )
+ return false
+ end
+
+
+ if ( seq8.get_name() != "Chain A, B. Thetaiotaomicron Susd With Maltotriose" )
+ return false
+ end
+ if ( seq8.get_accession != "pdb|3CKB|A" )
+ return false
+ end
+ if ( seq8.get_accession_source != "ncbi" )
+ return false
+ end
+ if ( seq8.get_taxonomy.get_name != "Bacteroides thetaiotaomicron" )
+ return false
+ end
+ if ( seq8.get_taxonomy.get_id != "818" )
+ return false
+ end
+ if ( seq8.get_taxonomy.get_id_source != "ncbi" )
+ return false
+ end
+
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_hmmsearch_domain_extractor()
+ begin
+ h = Evoruby::HmmsearchDomainExtractor.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_domain_sequence_extractor()
+ begin
+ h = Evoruby::DomainSequenceExtractor.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_hmmscan_parser()
+ begin
+ h = Evoruby::HmmscanParser.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_domains_to_forester()
+ begin
+ d = Evoruby::DomainsToForester.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+
+ def test_basic_table_parser()
+ begin
+ b = Evoruby::BasicTableParser.new()
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+
+ def test_cla()
+ begin
+ cla = CommandLineArguments.new( Array.new )
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_tree_puzzle()
+ begin
+ tp = TreePuzzle.new()
+ tp.run( '/home/czmasek/scratch/small.aln',
+ :wag,
+ :uniform,
+ 200 )
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+ def test_fastme()
+ begin
+ fastme = FastMe.new()
+ fastme.run( '/home/czmasek/scratch/outdist', 0, :GME )
+ rescue Exception => e
+ puts()
+ puts( e.to_s )
+ puts()
+ return false
+ end
+ return true
+ end
+
+
+ def run()
+
+ t0 = Time.now
+
+ puts
+ puts "ruby version " + RUBY_VERSION
+ puts Constants::EVORUBY + " version " + Constants::EVORUBY_VERSION
+ puts
+
+ path_to_evoruby = Test.get_path_to_evoruby()
+
+ if ( Util.is_string_empty?( path_to_evoruby ) )
+ path_to_evoruby = ""
+ puts()
+ puts( "Warning! Path to evoruby could not be established. Some tests will might fail." )
+ puts()
+ end
+
+ print( "--- Taxonomy: " )
+ if ( test_taxonomy() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- Sequence: " )
+ if ( test_sequence() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- Msa: " )
+ if ( test_msa() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- MsaFactory: " )
+ if ( test_msa_factory() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- DomainStructure: " )
+ if ( test_domain_structure() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- ProteinDomain: " )
+ if ( test_protein_domain() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- BasicTable: " )
+ if ( test_basic_table() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- MsaIO: " )
+ if ( test_msa_io )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- PhylipSequentialWriter: " )
+ if ( test_phylip_sequentialwriter )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- FastaWriter : " )
+ if ( test_fasta_writer )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- NexusWriter: " )
+ if ( test_nexus_writer )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- FastaParser: " )
+ if ( test_fasta_parser( path_to_evoruby ) )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- NCBI Tseq parser: " )
+ if ( test_ncbi_tseq_parser( path_to_evoruby ) )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- GeneralMsaParser: " )
+ if ( test_general_msa_parser( path_to_evoruby ) )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+
+ print( "--- Hmmsearch domain extractor: " )
+ if ( test_hmmsearch_domain_extractor )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- Domain sequence extractor: " )
+ if ( test_domain_sequence_extractor )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- Hmmscan parser: " )
+ if ( test_hmmscan_parser )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+
+ print( "--- Domains 2 forester: " )
+ if ( test_domains_to_forester )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- BasicTableParser: " )
+ if ( test_basic_table_parser )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- TreePuzzle (wrapper): " )
+ if ( test_tree_puzzle() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+ print( "--- FastMe (wrapper): " )
+ if ( test_fastme() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+
+
+
+ print( "--- CLA: " )
+ if ( test_cla() )
+ puts( "ok" )
+ @successes += 1
+ else
+ puts( "FAILED" )
+ @failures += 1
+ end
+ puts
+ puts "ruby version " + RUBY_VERSION
+ puts Constants::EVORUBY + " version " + Constants::EVORUBY_VERSION
+ puts
+
+ td = Time.at( Time.now - t0 )
+ puts( "Time : #{ td.sec }.#{ td.usec }s" )
+ puts()
+
+ puts( "Successful tests: " + @successes.to_s )
+ puts( "Failed tests : " + @failures.to_s )
+ puts()
+ if ( @failures < 1 )
+ puts( "OK" )
+ else
+ puts( "NOT ok" )
+ end
+
+ puts()
+ end
+
+ private
+
+ def Test.same?( n, m )
+ return ( ( n - m ).abs < 0.000001 )
+ end
+
+ def Test.get_path_to_evoruby()
+ rubylib = ENV['RUBYLIB'].split(':')
+ evoruby_path = nil
+ rubylib.each do | path |
+ if ( path =~ /evoruby/ )
+ evoruby_path = path
+ break
+ end
+ end
+ evoruby_path
+ end
+
+ end # class Test
+
+
+ test = Test.new()
+
+ test.run()
+
+
+end # module Evoruby
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = exe/tseq_tap
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: tseq_tap.rb,v 1.1 2008/12/31 06:00:08 cmzmasek Exp $
+
+
+require 'lib/evo/apps/tseq_taxonomy_processor'
+
+module Evoruby
+
+ tap = TseqTaxonomyProcessor.new()
+
+ tap.run()
+
+end # module Evoruby
--- /dev/null
+# $Id: 00_phylogeny_factory.template,v 1.9 2008/11/25 22:25:52 cmzmasek Exp $
+
+# Name convention if alignment specific parameters
+# are to be used (such as HMMs for hmmalign):
+# the substring before the first underscore is a
+# unique identifier and needs to match the identifiers
+# in '% <parameter-type> <unique-id>=<value>' statements
+# Example:
+# alignment name : 'bcl2_new_alignment'
+# parameter statments: '% HMM bcl2=Bcl2_ls'
+# '% RSL bcl2=60'
+$ PROBCONS=/home/czmasek/SOFTWARE/PROBCONS/probcons_v1_12/probcons
+$ DIALIGN_TX=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/source/dialign-tx
+$ DIALIGN_DIR=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.1/conf
+$ MAFFT=/home/czmasek/SOFTWARE/MAFFT/mafft-6.240/src/mafft
+$ T_COFFEE=/home/czmasek/SOFTWARE/T_COFFEE/T-COFFEE_distribution_Version_6.78/bin_linux/t_coffee
+$ MUSCLE=/home/czmasek/SOFTWARE/MUSCLE/muscle3.7/muscle
+$ CLUSTALW=/home/czmasek/SOFTWARE/CLUSTALW/clustalw-2.0.9/src/clustalw2
+$ KALIGN=/home/czmasek/SOFTWARE/KALIGN/kalign203/kalign
+$ HMMALIGN=/home/czmasek/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmalign
+$ MSA_PRO=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/msa_pro.rb
+$ PHYLO_PL=/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/perl/phylo_pl.pl
+
+# Default value is 40.
+% RSL SRCR=50
+% RSL NACHT=50
+% RSL TIR=60
+% RSL Bcl2=100
+% RSL homeobox=40
+
+% PHYLO_OPT=-WIB100q@1nxbwS21
+
+% TMP_DIR = /home/czmasek/tmp/
+
+# Need to give full path for HMM files.
+% HMM NACHT=/home/czmasek/DATA/PFAM/NACHT_ls_cz.hmm
+% HMM TIR=/home/czmasek/DATA/PFAM/PFAM_LS/TIR.ls.hmm
+% HMM SRCR=/home/czmasek/DATA/PFAM/PFAM_LS/SRCR.ls.hmm
+% HMM Homeobox=/home/czmasek/DATA/PFAM/PFAM_LS/Homeobox.ls.hmm
+% HMM Cofilin_ADF=/home/czmasek/DATA/PFAM/PFAM_LS/Cofilin_ADF.ls.hmm
+
+
+> KALIGN $ -o $_kalign
+> MSA_PRO -o=p -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_kalign_05_%[RSL]%.aln $_kalign_05_%[RSL]% %[TMP_DIR]%
+-
+
+> HMMALIGN -q -m -o $_hmmalign_m %[HMM]% $
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign_m $_hmmalign_m_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_m_05_%[RSL]%.aln $_hmmalign_m_05_%[RSL]% %[TMP_DIR]%
+-
+
+> HMMALIGN -q -o $_hmmalign %[HMM]% $
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_05_%[RSL]%.aln $_hmmalign_05_%[RSL]% %[TMP_DIR]%
+-
+
+> PROBCONS $ > $_probcons
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_probcons_05_%[RSL]%.aln $_probcons_05_%[RSL]% %[TMP_DIR]%
+-
+
+> DIALIGN_TX DIALIGN_DIR $ $_dialigntx
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_dialigntx_05_%[RSL]%.aln $_dialigntx_05_%[RSL]% %[TMP_DIR]%
+-
+
+> MAFFT --maxiterate 1000 --localpair --quiet $ > $_mafft
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_mafft_05_%[RSL]%.aln $_mafft_05_%[RSL]% %[TMP_DIR]%
+-
+
+#> T_COFFEE $ -outfile $_tcoffee
+#> rm $.dnd
+#> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.aln
+#> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_tcoffee $_tcoffee_05_%[RSL]%.nex
+#> PHYLO_PL %[PHYLO_OPT]% $_tcoffee_05_%[RSL]%.aln $_tcoffee_05_%[RSL]% %[TMP_DIR]%
+#> rm $.dnd
+#> rm $.html
+#-
+
+> MUSCLE -maxiters 1000 -maxtrees 100 -clw -in $ -out $_muscle
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]%
+-
+
+> CLUSTALW $ -outfile=$_clustalw
+> rm $.dnd
+> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.aln
+> MSA_PRO -o=n -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalw $_clustalw_05_%[RSL]%.nex
+> PHYLO_PL %[PHYLO_OPT]% $_clustalw_05_%[RSL]%.aln $_clustalw_05_%[RSL]% %[TMP_DIR]%
+> rm $.dnd
+-
--- /dev/null
+# $Id: 00_sample_tap_mapfile,v 1.2 2008/08/29 23:58:31 cmzmasek Exp $
+
+RAT#RAT
+Geodia cydonium#GEOCY
+Lubomirskia baicalensis#LUBBA
+Suberites domuncula#SUBDO
+Hydra vulgaris#HYDAT
+Apis mellifera#APIME
+Drosophila pseudoobscura#DROPS
+Aedes aegypti#AEDAE
+Tribolium castaneum#TRICA
+Caenorhabditis briggsae#CAEBR
+HUMAN#HUMAN
+Branchiostoma floridae#BRAFL
+amphioxus#BRAFL
+Brafl1#BRAFL
+Ciona intestinalis#CIOIN
+ciona#CIOIN
+cow#BOVIN
+dog#CANFA
+fugu#FUGRU
+mouse#MOUSE
+MOUSE#MOUSE
+Mus musculus#MOUSE
+Rattus norvegicus#RAT
+tetraodon#TETNG
+Tetraodon nigroviridis#TETNG
+urchin#STRPU
+Xenopus laevis#XENTR
+xenopus#XENTR
+zebrafish#BRARE
+Danio rerio#BRARE
+chicken#CHICK
+celegans#CAEEL
+Caenorhabditis elegans#CAEEL
+fruitfly#DROME
+Drosophila melanogaster#DROME
+Haemonchus contortus#HAECO
+Nematostella vectensis#NEMVE
+anemone#NEMVE
+human#HUMAN
+HUMAN#HUMAN
+Human#HUMAN
+Homo sapiens#HUMAN
+Chlamydomonas reinhardtii#CHLRE
+Monosiga brevicollis#MONBE
--- /dev/null
+7 26
+# 7 26 is not needed and ignored
+CLUSTAL
+PROBCONS
+>sequence 0
+ABCDEF
+>sequence 1
+a
+b
+c
+//comment
+d
+e
+!!comment
+f
+
+ > sequence 2
+123456
+ > sequence 3
+
+ a-c--f
+
--- /dev/null
+7 26
+# 7 26 is not needed and ignored
+
+
+sequence0 ABCDE GHIJ
+ KLMNOPQR TUVW
+sequence1 abcdefghi
+ jklm
+ nopq
+ rstu
+ vw
+sequence2 abcde
+ fghijkl---x_-*?_XX
+sequence3 12345678901234567890123
+
+ # this is_a_comment
+
+
+sequence4 ----------
+ -------------
+
+sequence5 a*c*ef****************w
+
+ % this is_another_comment
+
+sequence6 ururufhfghfgftgfhftgftt
+
+ // this is_yet_another_comment
+ !! this is_yet_another_comment
+
+ * -- *
+
+sequence0 a
+ bc
+sequence1 a
+ b
+ c
+sequence2 abc
+
+sequence3 abc
+ *..
+sequence4 ---
+sequence5 abc
+ ...
+sequence6 abc
+
+xy0
+xy1
+xy2
+xy3
+xy4
+xy5
+xy6
--- /dev/null
+<?xml version="1.0"?>
+<!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
+<TSeqSet>
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>29341016</TSeq_gi>
+ <TSeq_accver>AAO78806.1</TSeq_accver>
+ <TSeq_sid>gnl|mbpwusl|BT3701</TSeq_sid>
+ <TSeq_taxid>226186</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron VPI-5482</TSeq_orgname>
+ <TSeq_defline>SusD [Bacteroides thetaiotaomicron VPI-5482]</TSeq_defline>
+ <TSeq_length>551</TSeq_length>
+ <TSeq_sequence>MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>29349109</TSeq_gi>
+ <TSeq_accver>NP_812612.1</TSeq_accver>
+ <TSeq_sid>gnl|REF_mbpwusl|BT3701</TSeq_sid>
+ <TSeq_taxid>226186</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron VPI-5482</TSeq_orgname>
+ <TSeq_defline>SusD, outer membrane protein [Bacteroides thetaiotaomicron VPI-5482]</TSeq_defline>
+ <TSeq_length>551</TSeq_length>
+ <TSeq_sequence>MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>1478026</TSeq_gi>
+ <TSeq_accver>AAB42172.1</TSeq_accver>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>outer membrane protein</TSeq_defline>
+ <TSeq_length>554</TSeq_length>
+ <TSeq_sequence>MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPASHATYPDTDIPLFPFGRSIPDTCGSHFPPGRRRHRRHQLNFAKRAQLYKKGTEPLTEQETNRDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>188596440</TSeq_gi>
+ <TSeq_sid>pdb|3CK9|B</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain B, B. Thetaiotaomicron Susd With Maltoheptaose</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>188596439</TSeq_gi>
+ <TSeq_sid>pdb|3CK9|A</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain A, B. Thetaiotaomicron Susd With Maltoheptaose</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>171849127</TSeq_gi>
+ <TSeq_sid>pdb|3CKC|B</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain B, B. Thetaiotaomicron Susd</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSXIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>171849126</TSeq_gi>
+ <TSeq_sid>pdb|3CKC|A</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain A, B. Thetaiotaomicron Susd</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSXIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_gi>171849125</TSeq_gi>
+ <TSeq_sid>pdb|3CKB|B</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain B, B. Thetaiotaomicron Susd With Maltotriose</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+<TSeq>
+ <TSeq_seqtype value="protein"/>
+ <TSeq_sid>pdb|3CKB|A</TSeq_sid>
+ <TSeq_taxid>818</TSeq_taxid>
+ <TSeq_orgname>Bacteroides thetaiotaomicron</TSeq_orgname>
+ <TSeq_defline>Chain A, B. Thetaiotaomicron Susd With Maltotriose</TSeq_defline>
+ <TSeq_length>527</TSeq_length>
+ <TSeq_sequence>GINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+</TSeq>
+
+</TSeqSet>
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/apps/domain_sequence_extractor.rb - DomainSequenceExtractor class
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: domain_sequence_extractor.rb,v 1.19 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/io/parser/hmmsearch_domain_extractor'
+
+module Evoruby
+
+ class DomainSequenceExtractor
+
+ PRG_NAME = "dsx"
+ PRG_VERSION = "1.1.0"
+ PRG_DESC = "extraction of domain sequences from hmmsearch output"
+ PRG_DATE = "2008.01.03"
+ COPYRIGHT = "2008-2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ E_VALUE_THRESHOLD_OPTION = 'e'
+ LENGTH_THRESHOLD_OPTION = 'l'
+ ADD_POSITION_OPTION = 'p'
+ ADD_DOMAIN_NUMBER_OPTION = 'd'
+ ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT = 'dd'
+ ADD_DOMAIN_NUMBER_OPTION_AS_LETTER = 'dl'
+ TRIM_OPTION = 't'
+ LOG_FILE_SUFFIX = '_domain_seq_extr.log'
+ PASSED_SEQS_SUFFIX = '_domain_seq_extr_passed'
+ FAILED_SEQS_SUFFIX = '_domain_seq_extr_failed'
+ HELP_OPTION_1 = 'help'
+ HELP_OPTION_2 = 'h'
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC ,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ ld = Constants::LINE_DELIMITER
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, "error: " + $!, STDOUT )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 3 )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( E_VALUE_THRESHOLD_OPTION )
+ allowed_opts.push( ADD_POSITION_OPTION )
+ allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION )
+ allowed_opts.push( LENGTH_THRESHOLD_OPTION )
+ allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT )
+ allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION_AS_LETTER )
+ allowed_opts.push( TRIM_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ hmmsearch_output = cla.get_file_name( 0 )
+ fasta_sequence_file = cla.get_file_name( 1 )
+ outfile = cla.get_file_name( 2 )
+
+ add_position = false
+ if ( cla.is_option_set?( ADD_POSITION_OPTION ) )
+ add_position = true
+ end
+
+ trim = false
+ if ( cla.is_option_set?( TRIM_OPTION ) )
+ trim = true
+ end
+
+ add_domain_number = false
+ add_domain_number_as_letter = false
+ add_domain_number_as_digit = false
+
+ if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION ) )
+ add_domain_number = true
+ end
+ if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION_AS_LETTER ) )
+ add_domain_number_as_letter = true
+ end
+ if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT ) )
+ add_domain_number_as_digit = true
+ end
+
+ if ( add_domain_number_as_letter && add_domain_number_as_digit )
+ puts( "attempt to add domain number as letter and digit at the same time" )
+ print_help
+ exit( -1 )
+ end
+
+ e_value_threshold = -1.0
+ if ( cla.is_option_set?( E_VALUE_THRESHOLD_OPTION ) )
+ begin
+ e_value_threshold = cla.get_option_value_as_float( E_VALUE_THRESHOLD_OPTION )
+ rescue ArgumentError => e
+ Forester::Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ if ( e_value_threshold < 0.0 )
+ Forester::Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
+ end
+ end
+
+ length_threshold = -1
+ if ( cla.is_option_set?( LENGTH_THRESHOLD_OPTION ) )
+ begin
+ length_threshold = cla.get_option_value_as_int( LENGTH_THRESHOLD_OPTION )
+ rescue ArgumentError => e
+ Forester::Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ if ( length_threshold < 0)
+ Forester::Util.fatal_error( PRG_NAME, "attempt to use a negative length threshold", STDOUT )
+ end
+ end
+
+ log = String.new
+
+ puts()
+ puts( "Hmmsearch outputfile : " + hmmsearch_output )
+ log << "Hmmsearch outputfile : " + hmmsearch_output + ld
+ puts( "Fasta sequencefile (complete sequences): " + fasta_sequence_file )
+ log << "Fasta sequencefile (complete sequences): " + fasta_sequence_file + ld
+ puts( "Outputfile : " + outfile )
+ log << "Outputfile : " + outfile + ld
+ puts( "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX )
+ log << "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX + ld
+ puts( "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX )
+ log << "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX + ld
+ puts( "Logfile : " + outfile + LOG_FILE_SUFFIX )
+ log << "Logfile : " + outfile + LOG_FILE_SUFFIX + ld
+ if ( e_value_threshold >= 0.0 )
+ puts( "E-value threshold : " + e_value_threshold.to_s )
+ log << "E-value threshold : " + e_value_threshold.to_s + ld
+ else
+ puts( "E-value threshold : no threshold" )
+ log << "E-value threshold : no threshold" + ld
+ end
+ if ( length_threshold > 0 )
+ puts( "Length threshold : " + length_threshold.to_s )
+ log << "Length threshold : " + length_threshold.to_s + ld
+ else
+ puts( "Length threshold : no threshold" )
+ log << "Length threshold : no threshold" + ld
+ end
+
+ if ( trim )
+ puts( "Trim last 2 chars : true" )
+ log << "Trim last 2 chars : true" + ld
+ else
+ puts( "Trim names : false" )
+ log << "Trim names : false" + ld
+ end
+
+
+ if ( add_position )
+ puts( "Add positions (rel to complete seq) to extracted domains: true" )
+ log << "Add positions (rel to complete seq) to extracted domains: true" + ld
+ else
+ puts( "Add positions (rel to complete seq) to extracted domains: false" )
+ log << "Add positions (rel to complete seq) to extracted domains: false" + ld
+ end
+
+ if ( add_domain_number || add_domain_number_as_digit || add_domain_number_as_letter )
+ puts( "Add numbers to extracted domains (in case of more than one domain per complete seq): true" )
+ log << "Add numbers to extracted domains (in case of more than one domain per complete seq): true" + ld
+ else
+ puts( "Add numbers to extracted domains (in case of more than one domain per complete seq): false" )
+ log << "Add numbers to extracted domains (in case of more than one domain per complete seq): false" + ld
+ end
+
+ puts
+
+ domain_count = 0
+ begin
+ parser = HmmsearchDomainExtractor.new()
+ domain_count = parser.parse( hmmsearch_output,
+ fasta_sequence_file,
+ outfile,
+ outfile + PASSED_SEQS_SUFFIX,
+ outfile + FAILED_SEQS_SUFFIX,
+ e_value_threshold,
+ length_threshold,
+ add_position,
+ add_domain_number,
+ add_domain_number_as_digit,
+ add_domain_number_as_letter,
+ trim,
+ log )
+ rescue ArgumentError, IOError, StandardError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "unexpected exception!: " + e.to_s, STDOUT )
+ end
+
+ puts
+ Util.print_message( PRG_NAME, "extracted a total of " + domain_count.to_s + " domains" )
+ Util.print_message( PRG_NAME, "wrote; " + outfile )
+ Util.print_message( PRG_NAME, "wrote: " + outfile + LOG_FILE_SUFFIX )
+ Util.print_message( PRG_NAME, "(wrote: " + outfile + PASSED_SEQS_SUFFIX + ")" )
+ Util.print_message( PRG_NAME, "(wrote: " + outfile + FAILED_SEQS_SUFFIX + ")" )
+
+ begin
+ f = File.open( outfile + LOG_FILE_SUFFIX, 'a' )
+ f.print( log )
+ f.close
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ puts
+ Util.print_message( PRG_NAME, "OK" )
+ puts
+
+ end
+
+ def print_help()
+ puts()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <hmmsearch outputfile> <file containing complete sequences in fasta format> <outputfile>" )
+ puts()
+ puts( " options: -" + E_VALUE_THRESHOLD_OPTION + "=<f>: E-value threshold, default is no threshold" )
+ puts( " -" + LENGTH_THRESHOLD_OPTION + "=<i>: length threshold, default is no threshold" )
+ puts( " -" + ADD_POSITION_OPTION + ": to add positions (rel to complete seq) to extracted domains" )
+ puts( " -" + ADD_DOMAIN_NUMBER_OPTION + ": to add numbers to extracted domains (in case of more than one domain per complete seq) (example \"domain~2-3\")" )
+ puts( " -" + ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT + ": to add numbers to extracted domains as digit (example \"domain2\")" )
+ puts( " -" + ADD_DOMAIN_NUMBER_OPTION_AS_LETTER + ": to add numbers to extracted domains as letter (example \"domaina\")" )
+ puts( " -" + TRIM_OPTION + ": to remove the last 2 characters from sequence names" )
+ puts()
+ end
+
+ end # class DomainSequenceExtractor
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/domains_to_forester - DomainsToForester class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: domains_to_forester.rb,v 1.11 2010/12/13 19:00:11 cmzmasek Exp $
+#
+# last modified: 06/11/2007
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/sequence/protein_domain'
+require 'lib/evo/sequence/domain_structure'
+
+module Evoruby
+
+ class DomainsToForester
+
+ PRG_NAME = "d2f"
+ PRG_DESC = "parsed hmmpfam output to forester format"
+ PRG_VERSION = "1.0.0"
+ PRG_DATE = "2007.12.18"
+ COPYRIGHT = "2007 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ E_VALUE_THRESHOLD_OPTION = "e"
+ OVERWRITE_IF_SAME_FROM_TO_OPTION = "o"
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+ def parse( domains_list_file,
+ original_seqs_file,
+ outfile,
+ column_delimiter,
+ e_value_threshold,
+ overwrite_if_same_from_to )
+ Util.check_file_for_readability( domains_list_file )
+ Util.check_file_for_readability( original_seqs_file )
+ Util.check_file_for_writability( outfile )
+
+ domain_structures = Hash.new() # protein name is key, domain structure is value
+
+ f = MsaFactory.new
+
+ original_seqs = f.create_msa_from_file( original_seqs_file, FastaParser.new )
+ if ( original_seqs.get_number_of_seqs < 1 )
+ error_msg = "\"" + original_seqs_file + "\" appears devoid of sequences in fasta-format"
+ raise ArgumentError, error_msg
+ end
+
+ File.open( domains_list_file ) do | file |
+ while line = file.gets
+ if ( !is_ignorable?( line ) )
+ a = line.split( column_delimiter )
+ l = a.length
+ if ( ( l < 4 ) || ( e_value_threshold >= 0.0 && l < 5 ) )
+ error_msg = "unexpected format at line: " + line
+ raise IOError, error_msg
+ end
+ protein_name = a[ 0 ]
+ domain_name = a[ 1 ]
+ seq_from = -1
+ seq_to = -1
+ begin
+ seq_from = a[ 2 ].to_i
+ rescue Exception
+ error_msg = "failed to parse seq from from \"" + a[ 2 ] + "\" [line: " + line + "]"
+ raise IOError, error_msg
+ end
+ begin
+ seq_to = a[ 3 ].to_i
+ rescue Exception
+ error_msg = "failed to parse seq to from \"" + a[ 3 ] + "\" [line: " + line + "]"
+ raise IOError, error_msg
+ end
+
+ e_value = -1
+ if ( l > 4 )
+ begin
+ e_value = a[ 4 ].to_f
+ rescue Exception
+ error_msg = "failed to parse E-value from \"" + a[ 4 ] + "\" [line: " + line + "]"
+ raise IOError, error_msg
+ end
+ end
+
+ seq = original_seqs.get_by_name( protein_name, true, false )
+
+ total_length = seq.get_length
+
+ if ( ( ( e_value_threshold < 0.0 ) || ( e_value <= e_value_threshold ) ) )
+ pd = ProteinDomain.new( domain_name, seq_from, seq_to, "", e_value )
+ ds = nil
+ if ( domain_structures.has_key?( protein_name ) )
+ ds = domain_structures[ protein_name ]
+ else
+ ds = DomainStructure.new( total_length )
+ domain_structures[ protein_name ] = ds
+ end
+ ds.add_domain( pd, overwrite_if_same_from_to )
+ end
+
+ end
+ end
+ end
+
+ out = File.open( outfile, "a" )
+ ds = domain_structures.sort
+ for d in ds
+ protein_name = d[ 0 ]
+ domain_structure = d[ 1 ]
+ out.print( protein_name.to_s )
+ out.print( ":" )
+ out.print( domain_structure.to_NHX )
+ out.print( Constants::LINE_DELIMITER )
+ end
+
+ out.flush()
+ out.close()
+
+ end # parse
+
+
+
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 3 )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( E_VALUE_THRESHOLD_OPTION )
+ allowed_opts.push( OVERWRITE_IF_SAME_FROM_TO_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ domains_list_file = cla.get_file_name( 0 )
+ original_sequences_file = cla.get_file_name( 1 )
+ outfile = cla.get_file_name( 2 )
+
+
+ e_value_threshold = -1.0
+ if ( cla.is_option_set?( E_VALUE_THRESHOLD_OPTION ) )
+ begin
+ e_value_threshold = cla.get_option_value_as_float( E_VALUE_THRESHOLD_OPTION )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ if ( e_value_threshold < 0.0 )
+ Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
+ end
+ end
+ overwrite_if_same_from_to = false
+ if ( cla.is_option_set?( OVERWRITE_IF_SAME_FROM_TO_OPTION ) )
+ overwrite_if_same_from_to = true
+ end
+
+ puts()
+ puts( "Domains list file : " + domains_list_file )
+ puts( "Fasta sequencefile (complete sequences): " + original_sequences_file )
+ puts( "Outputfile : " + outfile )
+ if ( e_value_threshold >= 0.0 )
+ puts( "E-value threshold : " + e_value_threshold.to_s )
+ else
+ puts( "E-value threshold : no threshold" )
+ end
+ if ( overwrite_if_same_from_to )
+ puts( "Overwrite if same from and to : true" )
+ else
+ puts( "Overwrite if same from and to : false" )
+ end
+
+ puts
+
+ begin
+ parse( domains_list_file,
+ original_sequences_file,
+ outfile,
+ " ",
+ e_value_threshold,
+ overwrite_if_same_from_to )
+
+ rescue ArgumentError, IOError, StandardError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "unexpected exception: " + e.to_s, STDOUT )
+ end
+
+
+ puts
+ Util.print_message( PRG_NAME, 'OK' )
+ puts
+
+ end
+
+ private
+
+ def print_help()
+ puts()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <domains list file (parsed hmmpfam output)> <file containing complete sequences in fasta format> <outputfile>" )
+ puts()
+ puts( " options: -" + E_VALUE_THRESHOLD_OPTION + "=<f> : E-value threshold, default is no threshold" )
+ puts( " -" + OVERWRITE_IF_SAME_FROM_TO_OPTION + " : overwrite domain with same start and end with domain with better E-value" )
+ puts()
+ end
+
+
+
+ def is_ignorable?( line )
+ return ( line !~ /[A-Za-z0-9-]/ || line =~ /^\s*#/)
+ end
+
+
+ end # class DomainsToForester
+
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/evo_nursery.rb - EvoNursery class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: evo_nursery.rb,v 1.11 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+
+require 'lib/evo/soft/fastme'
+require 'lib/evo/soft/tree_puzzle'
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/io/parser/general_msa_parser'
+require 'lib/evo/io/writer/msa_writer'
+
+require 'iconv'
+
+module Evoruby
+
+ class EvoNursery
+ GAP_RATIO = 0.75
+ GAP_RATIO_FOR_SEQS = 0.75
+ MIN_LENGTH = 40
+ MIN_SEQS = 4
+ MAX_SEQS = 1600
+ MAX_ALN_FILE_SIZE = 4000000
+ MODEL = :auto
+ RATES = :uniform
+ FASTME_INITIAL_TREE = :GME
+ ALN_NAME = '_align_'
+ TREE_PUZZLE_OUTDIST = TreePuzzle::OUTDIST
+ TREE_PUZZLE_OUTFILE = TreePuzzle::OUTFILE
+ FASTME_OUTTREE = FastMe::OUTTREE
+ FASTME_OUTPUT_D = FastMe::OUTPUT_D
+
+ PRG_NAME = "evo_nursery"
+ PRG_DATE = "2009.10.15"
+ PRG_DESC = "pfam alignments to evolutionary trees"
+ PRG_VERSION = "0.20"
+ COPYRIGHT = "2009-2010 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+ def run
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ forester_home = Util.get_env_variable_value( Constants::FORESTER_HOME_ENV_VARIABLE )
+ java_home = Util.get_env_variable_value( Constants::JAVA_HOME_ENV_VARIABLE )
+ decorator = java_home + '/bin/java -cp ' + forester_home + '/java/forester.jar org.forester.application.decorator'
+
+ if ( ARGV == nil || ARGV.length != 1 )
+ help
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ help
+ exit( 0 )
+ end
+
+ output_dir = cla.get_file_name( 0 )
+
+ if output_dir !~ /\/$/
+ output_dir = output_dir + '/'
+ end
+
+ if !File.exists?( output_dir )
+ Util.fatal_error( PRG_NAME, output_dir.to_s + " does not exist", STDOUT )
+ end
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+ files = Dir.entries( "." )
+ skipped = Array.new
+ counter = 1
+ analyzed = 0;
+ begin
+ files.each { |pfam_aln_file|
+ if ( !File.directory?( pfam_aln_file ) &&
+ pfam_aln_file !~ /^\./ &&
+ pfam_aln_file !~ /.+\.tre$/ )
+
+ tree_out_file = output_dir + File.basename( pfam_aln_file ) + ".xml"
+
+ if File.exists?( tree_out_file )
+ puts
+ puts
+ puts "***** skipping " + File.basename( pfam_aln_file ) + ", already exists"
+ puts
+ skipped.push( File.basename( pfam_aln_file ) + " [already exists]" )
+ next
+ end
+
+ puts
+ puts counter.to_s + ": " + pfam_aln_file.to_str
+ counter += 1
+ if File.size( pfam_aln_file ) > MAX_ALN_FILE_SIZE
+ puts "***** skipping, file size: " + File.size( pfam_aln_file ).to_s
+ skipped.push( File.basename( pfam_aln_file ) + " [file size: " + File.size( pfam_aln_file ).to_s + "]" )
+ next
+ end
+
+ f = MsaFactory.new()
+ msa = f.create_msa_from_file( pfam_aln_file, GeneralMsaParser.new() )
+
+ if msa.get_number_of_seqs < MIN_SEQS || msa.get_number_of_seqs > MAX_SEQS
+ puts "***** skipping, seqs: " + msa.get_number_of_seqs.to_s
+ skipped.push( File.basename( pfam_aln_file ) + " [seqs: " + msa.get_number_of_seqs.to_s + "]" )
+ next
+ end
+
+ msa.remove_gap_columns_w_gap_ratio!( GAP_RATIO )
+
+ length = msa.get_length
+ if length < MIN_LENGTH
+ puts "***** skipping, length: " + length.to_s
+ skipped.push( File.basename( pfam_aln_file ) + " [length: " + length.to_s + "]" )
+ next
+ end
+
+ msa.remove_sequences_by_gap_ratio!( GAP_RATIO_FOR_SEQS )
+
+ if msa.get_number_of_seqs < MIN_SEQS
+ puts "***** skipping, seqs: " + msa.get_number_of_seqs.to_s
+ skipped.push( File.basename( pfam_aln_file ) + " [seqs: " + msa.get_number_of_seqs.to_s + "]" )
+ next
+ end
+
+ map_file = output_dir + File.basename( pfam_aln_file ) + ".map"
+ f = File.open( map_file, 'a' )
+ for i in 0 ... msa.get_number_of_seqs
+ name = msa.get_sequence( i ).get_name()
+ name =~ /(.+)_(.+)\/.+/
+ acc = $1
+ tax_code = $2
+
+ mapping_str = i.to_s
+ mapping_str << "\t"
+ mapping_str << 'TAXONOMY_CODE:'
+ mapping_str << tax_code
+ mapping_str << "\t"
+ mapping_str << 'SEQ_SYMBOL:'
+ mapping_str << ( acc + '_' + tax_code )
+ mapping_str << "\t"
+ if ( acc.length < 6 )
+ acc = acc + '_' + tax_code
+ end
+ mapping_str << 'SEQ_ACCESSION:'
+ mapping_str << acc
+ mapping_str << "\t"
+ mapping_str << 'SEQ_ACCESSION_SOURCE:UniProtKB'
+ mapping_str << "\t"
+ mapping_str << 'NODE_NAME:'
+ mapping_str << name
+ f.print( mapping_str )
+ f.print( "\n" )
+ name = msa.get_sequence( i ).set_name( i.to_s )
+ end
+ f.close
+
+ io = MsaIO.new()
+ w = MsaWriter
+ w = PhylipSequentialWriter.new()
+ w.clean( true )
+ w.set_max_name_length( 10 )
+ if File.exists?( output_dir + ALN_NAME )
+ File.unlink( output_dir + ALN_NAME )
+ end
+ io.write_to_file( msa, output_dir + ALN_NAME, w )
+
+ tp = TreePuzzle.new()
+ tp.run( output_dir + ALN_NAME,
+ MODEL,
+ RATES,
+ msa.get_number_of_seqs )
+
+ File.rename( output_dir + ALN_NAME, output_dir + File.basename( pfam_aln_file ) + ".aln" )
+
+ fastme = FastMe.new()
+ fastme.run( TREE_PUZZLE_OUTDIST, 0, FASTME_INITIAL_TREE )
+
+ pfam_acc = nil
+ pfam_de = nil
+ File.open( pfam_aln_file ) do |file|
+ while line = file.gets
+ line = ic.iconv( line )
+ if line =~ /^#=AC\s+(.+)/
+ pfam_acc = $1
+ end
+ if line =~ /^#=DE\s+(.+)/
+ pfam_de = $1
+ end
+ if pfam_acc && pfam_de
+ break
+ end
+ end
+ end
+ if !pfam_acc || !pfam_de
+ Util.fatal_error( PRG_NAME, "problem with " + pfam_aln_file.to_s, STDOUT )
+ end
+
+ puzzle_model = nil
+ File.open( TREE_PUZZLE_OUTFILE ) do |file|
+ while line = file.gets
+ line = ic.iconv( line )
+ if line =~ /^Model\s+of\s+substitution:\s+(.+)/
+ puzzle_model = $1
+ break
+ end
+ end
+ end
+ if !puzzle_model
+ Util.fatal_error( PRG_NAME, "problem with puzzle outfile: " + TREE_PUZZLE_OUTFILE.to_s, STDOUT )
+ end
+
+ desc = pfam_de
+ desc << ' | '
+ desc << 'ML pwd estimation by TREE-PUZZLE version '
+ desc << TreePuzzle::VERSION
+ desc << ', model: '
+ desc << puzzle_model
+ desc << ', rates: '
+ desc << RATES.to_s
+ desc << '; tree estimation by FastME version '
+ desc << FastMe::VERSION
+ desc << ', initial tree: '
+ desc << FASTME_INITIAL_TREE.to_s
+ desc << '; aln length: '
+ desc << msa.get_length.to_s
+
+ cmd = decorator + " -table -p -pn=\"" + pfam_aln_file +
+ "\" -pi=pfam:" + pfam_acc +
+ " -pd=\"" + desc + "\" " +
+ FASTME_OUTTREE + ' ' +
+ map_file + ' ' + tree_out_file
+
+ IO.popen( cmd , 'r+' ) do | pipe |
+ pipe.close_write
+ end
+ analyzed += 1
+
+ File.unlink( map_file )
+ File.unlink(TREE_PUZZLE_OUTDIST)
+ File.unlink( TREE_PUZZLE_OUTFILE )
+ File.unlink( FASTME_OUTPUT_D )
+ end
+ }
+ rescue ArgumentError, IOError, StandardError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ puts()
+ puts( 'Skipped:' )
+ puts()
+ for i in 0 ... skipped.size
+ puts i.to_s + ": " + skipped[ i ]
+ end
+
+ puts()
+ puts( 'Skipped : ' + skipped.size.to_s + ' alignments' )
+ puts( 'Analyzed: ' + analyzed.to_s + ' alignments' )
+
+ puts( 'Min gap ratio for col del : ' + GAP_RATIO.to_s )
+ puts( 'Min gap ratio for seq del : ' + GAP_RATIO_FOR_SEQS.to_s )
+ puts( 'Minimal aln length : ' + MIN_LENGTH.to_s )
+ puts( 'Minimal number of sequences: ' + MIN_SEQS.to_s )
+ puts( 'Maximal number of sequences: ' + MAX_SEQS.to_s )
+ puts( 'Maximal aln file size : ' + MAX_ALN_FILE_SIZE.to_s )
+ puts( 'Model : ' + MODEL.to_s )
+ puts( 'FastME initial tree: ' + FASTME_INITIAL_TREE.to_s )
+
+ puts()
+ puts( '[' + PRG_NAME + '] > OK' )
+ puts()
+
+ end # run
+
+ private
+
+ def help
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb <output dir> " )
+ puts()
+ end
+
+
+ end # class EvoNursery
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/apps/fasta_extractor.rb - FastaExtractor class
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fasta_extractor.rb,v 1.2 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/util'
+require 'lib/evo/util/constants'
+require 'lib/evo/util/command_line_arguments'
+
+
+module Evoruby
+
+ class FastaExtractor
+
+ PRG_NAME = "fae"
+ PRG_VERSION = "1.0.0"
+ PRG_DESC = "extraction of nucleotide sequences from a fasta file by names from wublast search"
+ PRG_DATE = "2008.08.09"
+ COPYRIGHT = "2008-2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+ HELP_OPTION_1 = 'help'
+ HELP_OPTION_2 = 'h'
+
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC ,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ ld = Constants::LINE_DELIMITER
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 3 )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ input_file = cla.get_file_name( 0 )
+ names_file = cla.get_file_name( 1 )
+ output_file = cla.get_file_name( 2 )
+
+ if !File.exist?( input_file )
+ Util.fatal_error( PRG_NAME, "error: input file [#{input_file}] does not exist" )
+ end
+ if !File.exist?( names_file )
+ Util.fatal_error( PRG_NAME, "error: names file [#{names_file}] does not exist" )
+ end
+ if File.exist?( output_file )
+ Util.fatal_error( PRG_NAME, "error: [#{output_file }] already exists" )
+ end
+
+ names = extract_names_with_frames( names_file )
+
+ extract_sequences( names, input_file, output_file )
+
+ puts
+ Util.print_message( PRG_NAME, "OK" )
+ puts
+
+ end
+
+
+ def extract_names_with_frames( names_file )
+ names = Hash.new()
+ File.open( names_file ) do | file |
+ while line = file.gets
+ if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
+ if ( line =~ /(\S+)\s+([+|-]\d)\s+\d+\s+(\S+)/ )
+ name = $1
+ frame = $2
+ e = $3
+ names[ name ] = "[" + frame + "] [" + e + "]"
+ end
+ end
+ end
+ end
+ names
+ end
+
+ def extract_sequences( names, fasta_file, output_file )
+ output = File.open( output_file, "a" )
+ matching_state = false
+ counter = 0
+ File.open( fasta_file ) do | file |
+ while line = file.gets
+ if !Util.is_string_empty?( line )
+ if ( line =~ /\s*>\s*(.+)/ )
+ name = $1
+ if names.has_key?( name )
+ matching_state = true
+ counter += 1
+ puts counter.to_s + ". " +name + " " + names[ name ]
+ output.print( ">" + name + " " + names[ name ] )
+ output.print( Evoruby::Constants::LINE_DELIMITER )
+ else
+ matching_state = false
+ end
+ elsif matching_state
+ output.print( line )
+ end
+ end
+ end
+ end
+ output.close()
+ end
+
+ def print_help()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb <input fasta file> <names file based on blast output> <output file>" )
+ puts()
+ end
+
+ end # class FastaExtractor
+end
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/apps/fasta_taxonomy_processor - FastaTaxonomyProcessor class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fasta_taxonomy_processor.rb,v 1.4 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/util'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/msa/msa'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/parser/sp_taxonomy_parser'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/apps/tseq_taxonomy_processor'
+
+module Evoruby
+
+ class FastaTaxonomyProcessor
+
+ PRG_NAME = "fasta_tap"
+ PRG_DATE = "2009.01.20"
+ PRG_DESC = "preprocessing of multiple sequence files in ncbi fasta format"
+ PRG_VERSION = "1.00"
+ COPYRIGHT = "2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ def initialize()
+ @tax_ids_to_sp_taxonomies = Hash.new()
+ end
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ARGV == nil || ARGV.length != 4
+ puts( "Usage: #{PRG_NAME}.rb <sp taxonomy file> <sequences in ncbi fasta format> <name for fasta outfile> <name for map outfile>" )
+ puts()
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ allowed_opts = Array.new
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+ end
+
+ sp_taxonomy_infile = cla.get_file_name( 0 )
+ sequences_infile = cla.get_file_name( 1 )
+ sequences_outfile = cla.get_file_name( 2 )
+ mapping_outfile = cla.get_file_name( 3 )
+
+ Util.fatal_error_if_not_readable( PRG_NAME, sp_taxonomy_infile )
+ Util.fatal_error_if_not_readable( PRG_NAME, sequences_infile )
+ Util.fatal_error_if_not_writable( PRG_NAME, mapping_outfile )
+ Util.fatal_error_if_not_writable( PRG_NAME, sequences_outfile )
+
+ sp_taxonomies = SpTaxonomyParser.parse( sp_taxonomy_infile )
+
+ Util.print_message( PRG_NAME, "read in taxonomic data for " + sp_taxonomies.size.to_s + " species from: " + sp_taxonomy_infile )
+
+ fasta_parser = FastaParser.new
+ msa_fac = MsaFactory.new
+
+ seqs = msa_fac.create_msa_from_file( sequences_infile, fasta_parser )
+
+ Util.print_message( PRG_NAME, "read in " + seqs.get_number_of_seqs.to_s + " sequences from: " + sequences_infile )
+
+ removed = seqs.remove_redundant_sequences!( true, true )
+
+ if removed.size > 0
+ Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
+ removed.each { | seq_name |
+ puts seq_name
+ }
+ Util.print_message( PRG_NAME, "will process " + seqs.get_number_of_seqs.to_s + " non-redundant sequences" )
+ end
+
+ mapping_out = File.open( mapping_outfile, "a" )
+
+ for i in 0 ... seqs.get_number_of_seqs
+ seq = seqs.get_sequence( i )
+ seq.set_name( Util::normalize_seq_name( modify_name( seq, i, sp_taxonomies, mapping_out ), 10 ) )
+ end
+
+ io = MsaIO.new()
+
+ w = FastaWriter.new()
+
+ w.set_max_name_length( 10 )
+ w.clean( true )
+ begin
+ io.write_to_file( seqs, sequences_outfile, w )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
+ end
+ mapping_out.close()
+
+ Util.print_message( PRG_NAME, "wrote: " + mapping_outfile )
+ Util.print_message( PRG_NAME, "wrote: " + sequences_outfile )
+ Util.print_message( PRG_NAME, "OK" )
+
+ end
+
+ private
+
+ def modify_name( seq, i, sp_taxonomies, mapping_outfile )
+
+ #i = i + 1792
+
+ seq_desc = seq.get_name
+
+ taxonomy_sn = nil
+
+ if seq_desc =~ /\[(.+)\]/
+ taxonomy_sn = $1
+ else
+ Util.fatal_error( PRG_NAME, "no taxonomy in [" + seq_desc + "]" )
+ end
+
+ matching_sp_taxonomy = nil
+
+ sp_taxonomies.each { |sp_taxonomy|
+ if ( sp_taxonomy.scientific_name == taxonomy_sn )
+ matching_sp_taxonomy = sp_taxonomy
+ end
+ }
+
+ if matching_sp_taxonomy == nil
+ Util.fatal_error( PRG_NAME, "taxonomy [" + taxonomy_sn + "] for [" + seq_desc + "] not found" )
+ end
+
+ new_name = i.to_s( 16 ) + "_" + matching_sp_taxonomy.code
+
+ gi = nil
+ if seq_desc =~ /gi\|(.+?)\|/
+ gi = $1
+ else
+ Util.fatal_error( PRG_NAME, "no gi in [" + seq_desc + "]" )
+ end
+
+ seq_name = ""
+
+ if seq_desc =~ /\|\s*([^|]+?)\s*\[/
+ seq_name = $1
+ end
+
+ if seq_name =~ /\[.+\]$/
+ # Redundant taxonomy information hides here.
+ seq_name = seq_name.sub(/\[.+\]$/, '')
+ end
+ if seq_name =~ /^\s*hypothetical\s+protein\s*/i
+ # Pointless information.
+ seq_name = seq_name.sub( /^\s*hypothetical\s+protein\s*/i, '' )
+ end
+ if seq_name =~ /^\s*conserved\s+hypothetical\s+protein\s*/i
+ # Pointless information.
+ seq_name = seq_name.sub( /^\s*conserved\s+hypothetical\s+protein\s*/i, '' )
+ end
+
+ if gi != nil
+ mapping_outfile.print( new_name + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_CODE + matching_sp_taxonomy.code + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_ID + matching_sp_taxonomy.id + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_ID_TYPE + "ncbi" + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_SN + matching_sp_taxonomy.scientific_name + "\t" +
+ TseqTaxonomyProcessor::SEQ_ACCESSION + gi.to_s + "\t" +
+ TseqTaxonomyProcessor::SEQ_ACCESSION_SOURCE + "gi" + "\t" +
+ TseqTaxonomyProcessor::SEQ_NAME + seq_name + "\t" +
+ TseqTaxonomyProcessor::SEQ_MOL_SEQ + seq.get_sequence_as_string +
+ Constants::LINE_DELIMITER )
+ else
+ mapping_outfile.print( new_name + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_CODE + matching_sp_taxonomy.code + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_ID + matching_sp_taxonomy.id + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_ID_TYPE + "ncbi" + "\t" +
+ TseqTaxonomyProcessor::TAXONOMY_SN + matching_sp_taxonomy.scientific_name + "\t" +
+ TseqTaxonomyProcessor::SEQ_NAME + seq_name + "\t" +
+ TseqTaxonomyProcessor::SEQ_MOL_SEQ + seq.get_sequence_as_string +
+ Constants::LINE_DELIMITER )
+
+ end
+ new_name
+ end
+
+ end
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/hmmscan_parser.rb - HmmscanParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
+#
+# last modified: 11/24/2009
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+
+module Evoruby
+
+ class HmmscanParser
+
+ PRG_NAME = "hsp"
+ PRG_VERSION = "1.0.1"
+ PRG_DESC = "hmmscan parser"
+ PRG_DATE = "2009.11.24"
+ COPYRIGHT = "2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ DELIMITER_OPTION = "d"
+ E_VALUE_THRESHOLD_OPTION = "e"
+ IGNORE_DUF_OPTION = "i"
+ PARSE_OUT_DESCRIPITION_OPTION = "a"
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+ def initialize
+ @domain_counts = Hash.new
+ end
+
+ # raises ArgumentError, IOError
+ def parse( inpath,
+ outpath,
+ column_delimiter,
+ e_value_threshold,
+ ignore_dufs,
+ get_descriptions )
+ Util.check_file_for_readability( inpath )
+ Util.check_file_for_writability( outpath )
+
+ outfile = File.open( outpath, "a" )
+
+ query = String.new
+ desc = String.new
+ model = String.new
+ env_from = String.new
+ env_to = String.new
+ i_e_value = String.new
+
+ queries_count = 0
+
+ nl = Constants::LINE_DELIMITER
+
+ File.open( inpath ) do | file |
+ while line = file.gets
+ if !HmmscanParser.is_ignorable?( line ) && line =~ /^\S+\s+\S/
+
+ # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
+ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
+ line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/
+
+ model = $1
+ query = $4
+ i_e_value = $13.to_f
+ env_from = $20.to_i
+ env_to = $21.to_i
+
+ if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
+ ( !ignore_dufs || ( model !~ /^DUF\d+/ ) ) )
+ count_model( model )
+ outfile.print( query +
+ column_delimiter )
+ if ( get_descriptions )
+ outfile.print( desc +
+ column_delimiter )
+ end
+ outfile.print( model +
+ column_delimiter +
+ env_from.to_s +
+ column_delimiter +
+ env_to.to_s +
+ column_delimiter +
+ i_e_value.to_s )
+ outfile.print( nl )
+ end
+ end
+ end # while line = file.gets
+ end
+ outfile.flush()
+ outfile.close()
+
+ return queries_count
+
+ end # def parse
+
+ def count_model( model )
+ if ( @domain_counts.has_key?( model ) )
+ count = @domain_counts[ model ].to_i
+ count += 1
+ @domain_counts[ model ] = count
+ else
+ @domain_counts[ model ] = 1
+ end
+ end
+
+
+ def get_domain_counts()
+ return @domain_counts
+ end
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 2 )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( DELIMITER_OPTION )
+ allowed_opts.push( E_VALUE_THRESHOLD_OPTION )
+ allowed_opts.push( IGNORE_DUF_OPTION )
+ allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ inpath = cla.get_file_name( 0 )
+ outpath = cla.get_file_name( 1 )
+
+ column_delimiter = "\t"
+ if ( cla.is_option_set?( DELIMITER_OPTION ) )
+ begin
+ column_delimiter = cla.get_option_value( DELIMITER_OPTION )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+
+ e_value_threshold = -1.0
+ if ( cla.is_option_set?( E_VALUE_THRESHOLD_OPTION ) )
+ begin
+ e_value_threshold = cla.get_option_value_as_float( E_VALUE_THRESHOLD_OPTION )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ if ( e_value_threshold < 0.0 )
+ Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
+ end
+ end
+
+ ignore_dufs = false
+ if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
+ ignore_dufs = true
+ end
+
+ parse_descriptions = false
+ if ( cla.is_option_set?( PARSE_OUT_DESCRIPITION_OPTION ) )
+ parse_descriptions = true
+ end
+
+ puts()
+ puts( "hmmpfam outputfile: " + inpath )
+ puts( "outputfile : " + outpath )
+ if ( e_value_threshold >= 0.0 )
+ puts( "E-value threshold : " + e_value_threshold.to_s )
+ else
+ puts( "E-value threshold : no threshold" )
+ end
+ if ( parse_descriptions )
+ puts( "parse descriptions: true" )
+ else
+ puts( "parse descriptions: false" )
+ end
+ if ( ignore_dufs )
+ puts( "ignore DUFs : true" )
+ else
+ puts( "ignore DUFs : false" )
+ end
+ if ( column_delimiter == "\t" )
+ puts( "column delimiter : TAB" )
+ else
+ puts( "column delimiter : " + column_delimiter )
+ end
+ puts()
+
+ begin
+ queries_count = parse( inpath,
+ outpath,
+ column_delimiter,
+ e_value_threshold,
+ ignore_dufs,
+ parse_descriptions )
+ rescue ArgumentError, IOError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ domain_counts = get_domain_counts()
+
+ puts
+ puts( "read output for a total of " + queries_count.to_s + " query sequences" )
+ puts
+ puts( "domain counts (considering potential E-value threshold and ignoring of DUFs):" )
+ puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
+ puts
+ puts( Util.draw_histogram( domain_counts, "#" ) )
+ puts
+ Util.print_message( PRG_NAME, 'OK' )
+ puts
+
+ end # def run()
+
+ def print_help()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <hmmscan outputfile> <outputfile>" )
+ puts()
+ puts( " options: -" + DELIMITER_OPTION + ": column delimiter for outputfile, default is TAB" )
+ puts( " -" + E_VALUE_THRESHOLD_OPTION + ": E-value threshold, default is no threshold" )
+ puts( " -" + PARSE_OUT_DESCRIPITION_OPTION + ": parse query description (in addition to query name)" )
+ puts( " -" + IGNORE_DUF_OPTION + ": ignore DUFs" )
+ puts()
+ end
+
+
+ private
+
+
+ def HmmscanParser.is_ignorable?( line )
+ return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
+ end
+
+ end # class HmmscanParser
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/apps/msa_processor.rb - MsaProcessor class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_processor.rb,v 1.33 2010/12/13 19:00:10 cmzmasek Exp $
+#
+
+require 'date'
+require 'set'
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/io/writer/nexus_writer'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/parser/general_msa_parser'
+require 'lib/evo/io/writer/msa_writer'
+
+module Evoruby
+
+ class MsaProcessor
+
+ PRG_NAME = "msa_pro"
+ PRG_DATE = "2010.03.19"
+ PRG_DESC = "processing of multiple sequence alignments"
+ PRG_VERSION = "1.05"
+ COPYRIGHT = "2008-2010 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+
+ NAME_LENGTH_DEFAULT = 10
+ WIDTH_DEFAULT_FASTA = 60
+ INPUT_TYPE_OPTION = "i"
+ OUTPUT_TYPE_OPTION = "o"
+ MAXIMAL_NAME_LENGTH_OPTION = "n"
+ WIDTH_OPTION = "w"
+ CLEAN_UP_SEQ_OPTION = "c"
+ REM_RED_OPTION = "rem_red"
+ REMOVE_GAP_COLUMNS_OPTION = "rgc"
+ REMOVE_GAP_ONLY_COLUMNS = "rgoc"
+ REMOVE_COLUMNS_GAP_RATIO_OPTION = "rr"
+ REMOVE_ALL_GAP_CHARACTERS_OPTION = "rg"
+ REMOVE_ALL_SEQUENCES_LISTED_OPTION = "r"
+ KEEP_ONLY_SEQUENCES_LISTED_OPTION = "k"
+
+ KEEP_MATCHING_SEQUENCES_OPTION = "mk"
+ REMOVE_MATCHING_SEQUENCES_OPTION = "mr"
+
+ TRIM_OPTION = "t"
+ REMOVE_SEQS_GAP_RATIO_OPTION = "rsgr"
+ REMOVE_SEQS_NON_GAP_LENGTH_OPTION = "rsl"
+ SPLIT = "split"
+ LOG_SUFFIX = "_msa_pro.log"
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+
+ def initialize()
+ @input_format_set = false
+ @output_format_set = false
+ @fasta_input = false
+ @phylip_input = true
+ @name_length = NAME_LENGTH_DEFAULT
+ @name_length_set = false
+ @width = WIDTH_DEFAULT_FASTA # fasta only
+ @pi_output = true
+ @fasta_output = false
+ @nexus_output = false
+ @clean = false # phylip only
+ @rgc = false
+ @rgoc = false
+ @rg = false # fasta only
+ @rem_red = false
+ @rgr = -1
+ @rsgr = -1
+ @rsl = -1
+ @remove_matching = nil
+ @keep_matching = nil
+
+ @seqs_name_file = nil
+ @remove_seqs = false
+ @keep_seqs = false
+ @trim = false
+ @split = -1
+ @first = -1
+ @last = -1
+ end
+
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ARGV.length < 1 )
+ Util.print_message( PRG_NAME, "Illegal number of arguments" )
+ print_help
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "Error: " + e.to_s, STDOUT )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 2 || ARGV.length < 2 )
+ Util.print_message( PRG_NAME, "Illegal number of arguments" )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( INPUT_TYPE_OPTION )
+ allowed_opts.push( OUTPUT_TYPE_OPTION )
+ allowed_opts.push( MAXIMAL_NAME_LENGTH_OPTION )
+ allowed_opts.push( WIDTH_OPTION )
+ allowed_opts.push( CLEAN_UP_SEQ_OPTION )
+ allowed_opts.push( REMOVE_GAP_COLUMNS_OPTION )
+ allowed_opts.push( REMOVE_GAP_ONLY_COLUMNS )
+ allowed_opts.push( REMOVE_COLUMNS_GAP_RATIO_OPTION )
+ allowed_opts.push( REMOVE_ALL_GAP_CHARACTERS_OPTION )
+ allowed_opts.push( REMOVE_ALL_SEQUENCES_LISTED_OPTION )
+ allowed_opts.push( KEEP_ONLY_SEQUENCES_LISTED_OPTION )
+ allowed_opts.push( TRIM_OPTION )
+ allowed_opts.push( REMOVE_SEQS_GAP_RATIO_OPTION )
+ allowed_opts.push( REMOVE_SEQS_NON_GAP_LENGTH_OPTION )
+ allowed_opts.push( SPLIT )
+ allowed_opts.push( REM_RED_OPTION )
+ allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
+ allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed )
+ end
+
+ input = cla.get_file_name( 0 )
+ output = cla.get_file_name( 1 )
+
+ analyze_command_line( cla )
+
+ begin
+ Util.check_file_for_readability( input )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ begin
+ Util.check_file_for_writability( output )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( @rg )
+ set_pi_output( false )
+ set_fasta_output( true )
+ set_nexus_output( false )
+ end
+
+ if ( !@input_format_set )
+ fasta_like = false
+ begin
+ fasta_like = Util.looks_like_fasta?( input )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ @fasta_input = fasta_like
+ @phylip_input = !fasta_like
+ if ( !@output_format_set )
+ @fasta_output = fasta_like
+ @pi_output = !fasta_like
+ @nexus_output = false
+ end
+ end
+
+ ld = Constants::LINE_DELIMITER
+ log = PRG_NAME + " " + PRG_VERSION + " [" + PRG_DATE + "]" + " LOG" + ld
+ now = DateTime.now
+ log << "Date/time: " + now.to_s + ld
+
+ puts()
+ puts( "Input alignment : " + input )
+ log << "Input alignment : " + input + ld
+ puts( "Output alignment : " + output )
+ log << "Output alignment : " + output + ld
+ if ( @phylip_input )
+ puts( "Input is : Phylip, or something like it" )
+ log << "Input is : Phylip, or something like it" + ld
+ elsif ( @fasta_input )
+ puts( "Input is : Fasta" )
+ log << "Input is : Fasta" + ld
+ end
+ if( @rgr >= 0 )
+ puts( "Max col gap ratio: " + @rgr.to_s )
+ log << "Max col gap ratio: " + @rgr.to_s + ld
+ elsif ( @rgc )
+ puts( "Remove gap colums" )
+ log << "Remove gap colums" + ld
+ elsif( @rgoc )
+ puts( "Remove gap only colums" )
+ log << "Remove gap only colums" + ld
+ end
+ if ( @clean )
+ puts( "Clean up : true" )
+ log << "Clean up : true" + ld
+ end
+
+ if ( @pi_output )
+ puts( "Output is : Phylip interleaved" )
+ log << "Output is : Phylip interleaved" + ld
+ elsif ( @fasta_output )
+ puts( "Output is : Fasta" )
+ log << "Output is : Fasta" + ld
+ if ( @width )
+ puts( "Width : " + @width.to_s )
+ log << "Width : " + @width.to_s + ld
+ end
+ if ( @rg )
+ puts( "Remove all gap characters (alignment is destroyed)" )
+ log << "Remove all gap characters (alignment is destroyed)" + ld
+ end
+ elsif ( @nexus_output )
+ puts( "Output is : Nexus" )
+ log << "Output is : Nexus" + ld
+ end
+ if ( @name_length_set || !@fasta_output )
+ puts( "Max name length : " + @name_length.to_s )
+ log << "Max name length : " + @name_length.to_s + ld
+ end
+ if( @rsgr >= 0 )
+ puts( "Remove sequences for which the gap ratio > " + @rsgr.to_s )
+ log << "Remove sequences for which the gap ratio > " + @rsgr.to_s + ld
+ end
+ if( @rsl >= 0 )
+ puts( "Remove sequences with less than " + @rsl.to_s + " non-gap characters" )
+ log << "Remove sequences with less than " + @rsl.to_s + " non-gap characters" + ld
+ end
+ if ( @remove_seqs )
+ puts( "Remove sequences listed in: " + @seqs_name_file )
+ log << "Remove sequences listed in: " + @seqs_name_file + ld
+ elsif ( @keep_seqs )
+ puts( "Keep only sequences listed in: " + @seqs_name_file )
+ log << "Keep only sequences listed in: " + @seqs_name_file + ld
+ end
+ if ( @trim )
+ puts( "Keep only columns from: "+ @first.to_s + " to " + @last.to_s )
+ log << "Keep only columns from: "+ @first.to_s + " to " + @last.to_s + ld
+ end
+ if ( @rem_red )
+ puts( "Remove redundant sequences: true" )
+ log << "Remove redundant sequences: true" + ld
+ end
+ if ( @split > 0 )
+ puts( "Split : " + @split.to_s )
+ log << "Split : " + @split.to_s + ld
+ end
+ puts()
+
+ f = MsaFactory.new()
+
+ msa = nil
+
+ begin
+ if ( @phylip_input )
+ msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
+ elsif ( @fasta_input )
+ msa = f.create_msa_from_file( input, FastaParser.new() )
+ end
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ if ( msa.is_aligned() )
+ Util.print_message( PRG_NAME, "Length of original alignment : " + msa.get_length.to_s )
+ log << "Length of original alignment : " + msa.get_length.to_s + ld
+ else
+ Util.print_message( PRG_NAME, "the input is not aligned" )
+ log << "The input is not aligned" + ld
+ end
+
+ all_names = Set.new()
+ for i in 0 ... msa.get_number_of_seqs()
+ current_name = msa.get_sequence( i ).get_name
+ if all_names.include?( current_name )
+ Util.print_warning_message( PRG_NAME, "sequence name [" + current_name + "] is not unique" )
+ else
+ all_names.add( current_name )
+ end
+ end
+
+ begin
+
+ if ( @remove_seqs || @keep_seqs )
+ names = Util.file2array( @seqs_name_file, true )
+ if ( names == nil || names.length() < 1 )
+ error_msg = "file \"" + @seqs_name_file.to_s + "\" appears empty"
+ Util.fatal_error( PRG_NAME, error_msg )
+ end
+
+ if ( @remove_seqs )
+ c = 0
+ for i in 0 ... names.length()
+ to_delete = msa.find_by_name( names[ i ], true, false )
+ if ( to_delete.length() < 1 )
+ error_msg = "sequence name \"" + names[ i ] + "\" not found"
+ Util.fatal_error( PRG_NAME, error_msg )
+ elsif ( to_delete.length() > 1 )
+ error_msg = "sequence name \"" + names[ i ] + "\" is not unique"
+ Util.fatal_error( PRG_NAME, error_msg )
+ else
+ msa.remove_sequence!( to_delete[ 0 ] )
+ c += 1
+ end
+ end
+ Util.print_message( PRG_NAME, "Removed " + c.to_s + " sequences" )
+ log << "Removed " + c.to_s + " sequences" + ld
+ elsif ( @keep_seqs )
+ msa_new = Msa.new()
+ r = 0
+ k = 0
+ for j in 0 ... msa.get_number_of_seqs()
+ if ( names.include?( msa.get_sequence( j ).get_name() ) )
+ msa_new.add_sequence( msa.get_sequence( j ) )
+ k += 1
+ else
+ r += 1
+ end
+ end
+ msa = msa_new
+ Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
+ log << "Kept " + k.to_s + " sequences" + ld
+ Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
+ log << "removed " + r.to_s + " sequences" + ld
+ end
+ end
+
+ if ( @trim )
+ msa.trim!( @first, @last )
+ end
+ if( @rgr >= 0 )
+ msa.remove_gap_columns_w_gap_ratio!( @rgr )
+ elsif ( @rgc )
+ msa.remove_gap_columns!()
+ elsif( @rgoc )
+ msa.remove_gap_only_columns!()
+ end
+ if( @rsgr >= 0 )
+ n = msa.get_number_of_seqs()
+ removed = msa.remove_sequences_by_gap_ratio!( @rsgr )
+ k = msa.get_number_of_seqs()
+ r = n - k
+ Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
+ log << "Kept " + k.to_s + " sequences" + ld
+ Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
+ log << "Removed " + r.to_s + " sequences:" + ld
+ removed.each { | seq_name |
+ log << " " + seq_name + ld
+ }
+ end
+ if( @rsl >= 0 )
+ n = msa.get_number_of_seqs()
+ removed = msa.remove_sequences_by_non_gap_length!( @rsl )
+ k = msa.get_number_of_seqs()
+ r = n - k
+ Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
+ log << "Kept " + k.to_s + " sequences" + ld
+ Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
+ log << "Removed " + r.to_s + " sequences:" + ld
+ removed.each { | seq_name |
+ log << " " + seq_name + ld
+ }
+ end
+ if ( @keep_matching )
+ n = msa.get_number_of_seqs
+ to_be_removed = Set.new
+ for ii in 0 ... n
+ seq = msa.get_sequence( ii )
+ if !seq.get_name.downcase.index( @keep_matching.downcase )
+ to_be_removed.add( ii )
+ end
+ end
+ to_be_removed_ary = to_be_removed.to_a.sort.reverse
+ to_be_removed_ary.each { | index |
+ msa.remove_sequence!( index )
+ }
+ # msa = sort( msa )
+ end
+ if ( @remove_matching )
+ n = msa.get_number_of_seqs
+ to_be_removed = Set.new
+ for iii in 0 ... n
+
+ seq = msa.get_sequence( iii )
+
+ if seq.get_name.downcase.index( @remove_matching.downcase )
+ to_be_removed.add( iii )
+ end
+ end
+ to_be_removed_ary = to_be_removed.to_a.sort.reverse
+ to_be_removed_ary.each { | index |
+ msa.remove_sequence!( index )
+ }
+ msa = sort( msa )
+ end
+
+
+
+ if ( @split > 0 )
+ begin
+ msas = msa.split( @split, true )
+ io = MsaIO.new()
+ w = MsaWriter
+ if ( @pi_output )
+ w = PhylipSequentialWriter.new()
+ w.clean( @clean )
+ w.set_max_name_length( @name_length )
+ elsif( @fasta_output )
+ w = FastaWriter.new()
+ w.set_line_width( @width )
+ if ( @rg )
+ w.remove_gap_chars( true )
+ Util.print_warning_message( PRG_NAME, "removing gap character, the output is likely to become unaligned" )
+ log << "removing gap character, the output is likely to become unaligned" + ld
+ end
+ w.clean( @clean )
+ if ( @name_length_set )
+ w.set_max_name_length( @name_length )
+ end
+ elsif( @nexus_output )
+ w = NexusWriter.new()
+ w.clean( @clean )
+ w.set_max_name_length( @name_length )
+ end
+ i = 0
+ for m in msas
+ i = i + 1
+ io.write_to_file( m, output + "_" + i.to_s, w )
+ end
+ Util.print_message( PRG_NAME, "wrote " + msas.length.to_s + " files" )
+ log << "wrote " + msas.length.to_s + " files" + ld
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ end
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ if ( @split <= 0 )
+
+ unless ( @rg )
+ if ( msa.is_aligned() )
+ Util.print_message( PRG_NAME, "length of processed alignment: " + msa.get_length.to_s )
+ log << "length of processed alignment: " + msa.get_length.to_s + ld
+ else
+ Util.print_warning_message( PRG_NAME, "output is not aligned" )
+ log << "output is not aligned" + ld
+ end
+ end
+
+ if @rem_red
+ removed = msa.remove_redundant_sequences!( true, true )
+ if removed.size > 0
+ Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
+ log << "going to ignore the following " + removed.size.to_s + " redundant sequences:" + ld
+ removed.each { | seq_name |
+ puts seq_name
+ log << seq_name + ld
+ }
+ Util.print_message( PRG_NAME, "will store " + msa.get_number_of_seqs.to_s + " non-redundant sequences" )
+ log << "will store " + msa.get_number_of_seqs.to_s + " non-redundant sequences" + ld
+ end
+ end
+
+ io = MsaIO.new()
+
+ w = MsaWriter
+
+ if ( @pi_output )
+ w = PhylipSequentialWriter.new()
+ w.clean( @clean )
+ w.set_max_name_length( @name_length )
+ elsif( @fasta_output )
+ w = FastaWriter.new()
+ w.set_line_width( @width )
+ if ( @rg )
+ w.remove_gap_chars( true )
+ Util.print_warning_message( PRG_NAME, "removing gap characters, the output is likely to become unaligned" )
+ log << "removing gap character, the output is likely to become unaligned" + ld
+ end
+ w.clean( @clean )
+ if ( @name_length_set )
+ w.set_max_name_length( @name_length )
+ end
+ elsif( @nexus_output )
+ w = NexusWriter.new()
+ w.clean( @clean )
+ w.set_max_name_length( @name_length )
+ end
+
+
+ begin
+ io.write_to_file( msa, output, w )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ begin
+ f = File.open( output + LOG_SUFFIX, 'a' )
+ f.print( log )
+ f.close
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+
+ end
+ Util.print_message( PRG_NAME, "OK" )
+ puts
+ end
+
+
+ private
+
+ def sort( msa )
+ names = Set.new
+ for i in 0 ... msa.get_number_of_seqs
+ name = msa.get_sequence( i ).get_name
+ names.add( name )
+ end
+ sorted_ary = names.to_a.sort
+ new_msa = Msa.new
+ sorted_ary.each { | seq_name |
+ seq = msa.get_sequence( msa.find_by_name( seq_name, true, false )[ 0 ] )
+ new_msa.add_sequence( seq )
+ }
+ new_msa
+ end
+
+ def set_fasta_input( fi = true )
+ @fasta_input = fi
+ @input_format_set = true
+ end
+ def set_phylip_input( pi = true )
+ @phylip_input = pi
+ @input_format_set = true
+ end
+ def set_name_length( i )
+ @name_length = i
+ @name_length_set = true
+ end
+ def set_width( i )
+ @width = i
+ end
+ def set_fasta_output( fo = true )
+ @fasta_output = fo
+ @output_format_set = true
+ end
+ def set_pi_output( pso = true )
+ @pi_output = pso
+ @output_format_set = true
+ end
+ def set_nexus_output( nexus = true )
+ @nexus_output = nexus
+ @output_format_set = true
+ end
+ def set_clean( c = true )
+ @clean = c
+ end
+ def set_remove_gap_columns( rgc = true )
+ @rgc = rgc
+ end
+ def set_remove_gap_only_columns( rgoc = true )
+ @rgoc = rgoc
+ end
+ def set_remove_gaps( rg = true )
+ @rg = rg
+ end
+ def set_remove_gap_ratio( rgr )
+ @rgr = rgr
+ end
+ def set_remove_seqs_gap_ratio( rsgr )
+ @rsgr = rsgr
+ end
+ def set_remove_seqs_min_non_gap_length( rsl )
+ @rsl = rsl
+ end
+ def set_remove_seqs( file )
+ @seqs_name_file = file
+ @remove_seqs = true
+ @keep_seqs = false
+ end
+ def set_keep_seqs( file )
+ @seqs_name_file = file
+ @keep_seqs = true
+ @remove_seqs = false
+ end
+ def set_trim( first, last )
+ @trim = true
+ @first = first
+ @last = last
+ end
+ def set_remove_matching( remove )
+ @remove_matching = remove
+ end
+ def set_keep_matching( keep )
+ @keep_matching = keep
+ end
+ def set_rem_red( rr )
+ @rem_red = rr
+ end
+
+
+
+ def set_split( s )
+ if ( s > 0 )
+ @split = s
+ @clean = false # phylip only
+ @rgc = false
+ @rgoc = false
+ @rg = false # fasta only
+ @rgr = -1
+ @rsgr = -1
+ @rsl = -1
+ @seqs_name_file = nil
+ @remove_seqs = false
+ @keep_seqs = false
+ @trim = false
+ @first = -1
+ @last = -1
+ end
+ end
+ def analyze_command_line( cla )
+ if ( cla.is_option_set?( INPUT_TYPE_OPTION ) )
+ begin
+ type = cla.get_option_value( INPUT_TYPE_OPTION )
+ if ( type == "p" )
+ set_phylip_input( true )
+ set_fasta_input( false )
+ elsif ( type == "f" )
+ set_fasta_input( true )
+ set_phylip_input( false )
+ end
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( OUTPUT_TYPE_OPTION ) )
+ begin
+ type = cla.get_option_value( OUTPUT_TYPE_OPTION )
+ if ( type == "p" )
+ set_pi_output( true )
+ set_fasta_output( false )
+ set_nexus_output( false )
+ elsif ( type == "f" )
+ set_pi_output( false )
+ set_fasta_output( true )
+ set_nexus_output( false )
+ elsif ( type == "n" )
+ set_pi_output( false )
+ set_fasta_output( false )
+ set_nexus_output( true )
+ end
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( MAXIMAL_NAME_LENGTH_OPTION ) )
+ begin
+ l = cla.get_option_value_as_int( MAXIMAL_NAME_LENGTH_OPTION )
+ set_name_length( l )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( WIDTH_OPTION ) )
+ begin
+ w = cla.get_option_value_as_int( WIDTH_OPTION )
+ set_width( w )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( CLEAN_UP_SEQ_OPTION ) )
+ set_clean( true )
+ end
+ if ( cla.is_option_set?( REMOVE_GAP_COLUMNS_OPTION ) )
+ set_remove_gap_columns( true )
+ end
+ if ( cla.is_option_set?( REM_RED_OPTION ) )
+ set_rem_red( true )
+ end
+ if ( cla.is_option_set?( REMOVE_GAP_ONLY_COLUMNS ) )
+ set_remove_gap_only_columns( true )
+ end
+ if ( cla.is_option_set?( REMOVE_ALL_GAP_CHARACTERS_OPTION ) )
+ set_remove_gaps( true )
+ end
+ if ( cla.is_option_set?( REMOVE_COLUMNS_GAP_RATIO_OPTION ) )
+ begin
+ f = cla.get_option_value_as_float( REMOVE_COLUMNS_GAP_RATIO_OPTION )
+ set_remove_gap_ratio( f )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( REMOVE_ALL_SEQUENCES_LISTED_OPTION ) )
+ begin
+ s = cla.get_option_value( REMOVE_ALL_SEQUENCES_LISTED_OPTION )
+ set_remove_seqs( s )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( KEEP_ONLY_SEQUENCES_LISTED_OPTION ) )
+ begin
+ s = cla.get_option_value( KEEP_ONLY_SEQUENCES_LISTED_OPTION )
+ set_keep_seqs( s )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( TRIM_OPTION ) )
+ begin
+ s = cla.get_option_value( TRIM_OPTION )
+ if ( s =~ /(\d+)-(\d+)/ )
+ set_trim( $1.to_i(), $2.to_i() )
+ else
+ puts( "illegal argument" )
+ print_help
+ exit( -1 )
+ end
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( REMOVE_SEQS_GAP_RATIO_OPTION ) )
+ begin
+ f = cla.get_option_value_as_float( REMOVE_SEQS_GAP_RATIO_OPTION )
+ set_remove_seqs_gap_ratio( f )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( REMOVE_SEQS_NON_GAP_LENGTH_OPTION ) )
+ begin
+ f = cla.get_option_value_as_int( REMOVE_SEQS_NON_GAP_LENGTH_OPTION )
+ set_remove_seqs_min_non_gap_length( f )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( SPLIT ) )
+ begin
+ s = cla.get_option_value_as_int( SPLIT )
+ set_split( s )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+
+ end
+ if ( cla.is_option_set?( REMOVE_MATCHING_SEQUENCES_OPTION ) )
+ begin
+ s = cla.get_option_value( REMOVE_MATCHING_SEQUENCES_OPTION )
+ set_remove_matching( s )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+ if ( cla.is_option_set?( KEEP_MATCHING_SEQUENCES_OPTION ) )
+ begin
+ s = cla.get_option_value( KEEP_MATCHING_SEQUENCES_OPTION )
+ set_keep_matching( s )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+
+
+ end
+
+ def print_help()
+ puts()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <input alignment> <output>" )
+ puts()
+ puts( " options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
+ puts( " -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
+ puts( " -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
+ puts( " -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
+ puts( " -" + CLEAN_UP_SEQ_OPTION + ": clean up sequences" )
+ puts( " -" + REMOVE_GAP_COLUMNS_OPTION + ": remove gap columns" )
+ puts( " -" + REMOVE_GAP_ONLY_COLUMNS + ": remove gap-only columns" )
+ puts( " -" + REMOVE_COLUMNS_GAP_RATIO_OPTION + "=<n>: remove columns for which ( seqs with gap / number of sequences > n )" )
+ puts( " -" + REMOVE_ALL_GAP_CHARACTERS_OPTION + ": remove all gap characters (destroys alignment, fasta output only)" )
+ puts( " -" + REMOVE_ALL_SEQUENCES_LISTED_OPTION + "=<file>: remove all sequences listed in file" )
+ puts( " -" + KEEP_ONLY_SEQUENCES_LISTED_OPTION + "=<file>: keep only sequences listed in file" )
+ puts( " -" + TRIM_OPTION + "=<first>-<last>: remove columns before first and after last" )
+ puts( " -" + REMOVE_SEQS_GAP_RATIO_OPTION + "=<n>: remove sequences for which the gap ratio > n (after column operations)" )
+ puts( " -" + REMOVE_SEQS_NON_GAP_LENGTH_OPTION + "=<n> remove sequences with less than n non-gap characters (after column operations)" )
+ puts( " -" + REMOVE_MATCHING_SEQUENCES_OPTION + "=<s> remove all sequences with names containing s" )
+ puts( " -" + KEEP_MATCHING_SEQUENCES_OPTION + "=<s> keep only sequences with names containing s" )
+ puts( " -" + SPLIT + "=<n> split a fasta file into n files of equal number of sequences (expect for " )
+ puts( " last one), cannot be used with other options" )
+ puts( " -" + REM_RED_OPTION + ": remove redundant sequences" )
+ puts()
+ end
+
+
+
+
+
+ end # class MsaProcessor
+
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/multi_sequence_extractor.rb - MultiSequenceExtractor class
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: multi_sequence_extractor.rb,v 1.10 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/msa/msa'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/util/command_line_arguments'
+
+
+
+module Evoruby
+
+ class MultiSequenceExtractor
+
+ PRG_NAME = "mse"
+ PRG_VERSION = "1.0.0"
+ PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
+ PRG_DATE = "2008.08.13"
+ COPYRIGHT = "2008-2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+ HELP_OPTION_1 = 'help'
+ HELP_OPTION_2 = 'h'
+
+ LOG_SUFFIX = ".mse_log"
+ FASTA_SUFFIX = ".fasta"
+ FASTA_WITH_NORMALIZED_IDS_SUFFIX = ".ni.fasta"
+ NORMALIZED_IDS_MAP_SUFFIX = ".nim"
+ PROTEINS_LIST_FILE_SEPARATOR = "\t"
+ CACHE_GENOMES = false
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC ,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ ld = Constants::LINE_DELIMITER
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if ( cla.get_number_of_files != 3 && cla.get_number_of_files != 4 )
+ print_help
+ exit( -1 )
+ end
+
+ allowed_opts = Array.new
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ seq_names_files_suffix = cla.get_file_name( 0 )
+ input_dir = cla.get_file_name( 1 )
+ out_dir = cla.get_file_name( 2 )
+ mapping_file = nil
+
+ if ( cla.get_number_of_files == 4 )
+ mapping_file = cla.get_file_name( 3 )
+ begin
+ Util.check_file_for_readability( mapping_file )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ end
+
+ if !File.exist?( input_dir )
+ Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
+ end
+ if !File.exist?( out_dir )
+ Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
+ end
+ if !File.directory?( input_dir )
+ Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
+ end
+ if !File.directory?( out_dir )
+ Util.fatal_error( PRG_NAME, "error: [#{out_dir}] is not a directory" )
+ end
+
+
+ log = String.new
+
+ log << "Program : " + PRG_NAME + ld
+ log << "Version : " + PRG_VERSION + ld
+ log << "Program date : " + PRG_DATE + ld
+
+ puts()
+ puts( "Sequence names files suffix: " + seq_names_files_suffix )
+ log << "Sequence names files suffix: " + seq_names_files_suffix + ld
+ puts( "Input dir : " + input_dir )
+ log << "Input dir : " + input_dir + ld
+ puts( "Output dir : " + out_dir )
+ log << "Output dir : " + out_dir + ld
+ if ( mapping_file != nil )
+ puts( "Mapping file : " + mapping_file )
+ log << "Mapping file : " + mapping_file + ld
+ end
+ log << "Date : " + Time.now.to_s + ld
+ puts
+
+ if ( mapping_file != nil )
+ species_codes_to_paths = extract_mappings( mapping_file )
+ end
+
+ input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
+
+ counter = 0
+ species_to_genomes = Hash.new()
+
+ input_files.each { |input_file|
+ counter += 1
+ puts
+ puts
+ puts counter.to_s + "/" + input_files.size.to_s
+ read_seq_family_file( input_file,
+ seq_names_files_suffix,
+ input_dir,
+ species_codes_to_paths,
+ species_to_genomes,
+ log,
+ out_dir,
+ mapping_file )
+ }
+ puts
+ Util.print_message( PRG_NAME, "OK" )
+ puts
+
+ end
+
+
+ def read_seq_family_file( input_file,
+ seq_names_files_suffix,
+ input_dir,
+ species_codes_to_paths,
+ species_to_genomes,
+ log,
+ out_dir,
+ mapping_file )
+
+ begin
+ Util.check_file_for_readability( input_file )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ basename = File.basename( input_file, seq_names_files_suffix )
+ out_file_path_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
+ out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
+ out_file_path_ids_map = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
+ begin
+ Util.check_file_for_writability( out_file_path_fasta_file )
+ Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
+ Util.check_file_for_writability( out_file_path_ids_map )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ ids_map_writer = nil
+ begin
+ ids_map_writer = File.open( out_file_path_ids_map, 'a' )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ current_species = ""
+ current_msa = nil
+ new_msa = Msa.new
+ new_msa_normalized_ids = Msa.new
+ per_species_counter = 0
+
+ puts basename
+
+ File.open( input_file ) do | file |
+ while line = file.gets
+ if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
+ values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
+ if ( values.length < 2 )
+ Util.fatal_error( PRG_NAME, "unexpected format: " + line )
+ end
+ species = values[ 0 ]
+ seq_name = values[ 1 ]
+ if ( species != current_species )
+ current_species = species
+ my_file = input_dir + Constants::FILE_SEPARATOR + current_species
+
+ if ( !File.exist?( my_file ) )
+ if species_codes_to_paths == nil
+ Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
+ elsif ( !species_codes_to_paths.has_key?( current_species ) )
+ Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
+ end
+ my_file = species_codes_to_paths[ current_species ]
+ end
+ my_path = File.expand_path( my_file )
+ my_readlink = my_path
+ if ( File.symlink?( my_path ) )
+ my_readlink = File.readlink( my_path )
+ end
+ current_msa = nil
+ if ( CACHE_GENOMES && species_to_genomes.has_key?( species ) )
+ current_msa = species_to_genomes[ species ]
+ else
+ current_msa = read_fasta_file( my_file )
+ if CACHE_GENOMES
+ species_to_genomes[ species ] = current_msa
+ end
+ end
+
+ if ( per_species_counter > 0 )
+ print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
+ per_species_counter = 0
+ end
+ puts " " + current_species + " [" + my_readlink + "]"
+ log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+ end
+ puts " " + seq_name
+ log << " " + seq_name + Constants::LINE_DELIMITER
+ per_species_counter = per_species_counter + 1
+ seq = nil
+
+ if current_msa.find_by_name_start( seq_name, true ).size > 0
+ begin
+ seq = current_msa.get_by_name_start( seq_name, true ).copy
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ elsif
+ # Not found, try finding by partial match.
+ begin
+ seq = current_msa.get_by_name( seq_name, true, true )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ end
+
+ normalized_id = per_species_counter.to_s( 16 ).upcase +
+ "_" + current_species
+
+ per_species_counter.to_i
+
+ ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
+
+ if ( seq != nil )
+ seq.set_name( seq.get_name + " [" + current_species + "]" )
+ new_msa.add_sequence( seq )
+ else
+ Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
+ end
+
+ new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
+
+ end
+ end
+
+ end
+
+ ids_map_writer.close
+
+ if ( per_species_counter > 0 )
+ print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
+ end
+
+ io = MsaIO.new()
+
+ fasta_writer = FastaWriter.new()
+ fasta_writer.remove_gap_chars
+ fasta_writer.clean
+
+ begin
+ io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ begin
+ io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ begin
+ f = File.open( out_dir + Constants::FILE_SEPARATOR + basename + LOG_SUFFIX , 'a' )
+ f.print( log )
+ f.close
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ end
+
+ def obtain_inputfiles( input_dir, seq_names_files_suffix )
+ input_files = Array.new()
+ Dir.foreach( input_dir ) { |file_name|
+ if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
+ input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
+ end
+ }
+ input_files
+ end
+
+ def extract_mappings( mapping_file )
+ species_code_to_path = Hash.new()
+ File.open( mapping_file ) do | file |
+ while line = file.gets
+ if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
+ if ( line =~ /(\S+)\s+(\S+)/ )
+ species = $1
+ path = $2
+ if ( species_code_to_path.has_key?( species ) )
+ Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
+ end
+ if ( species_code_to_path.has_value?( path ) )
+ Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
+ end
+ if ( !File.exist?( path ) )
+ Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
+ end
+ if ( !File.file?( path ) )
+ Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
+ end
+ if ( !File.readable?( path ) )
+ Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
+ end
+ if ( File.size( path ) < 10000 )
+ Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
+ end
+ if ( !Util.looks_like_fasta?( path ) )
+ Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
+ end
+ species_code_to_path[ species ] = path
+ puts species + " -> " + path
+ end
+ end
+ end
+ end
+ species_code_to_path
+ end
+
+ def print_counts( per_species_counter, log, ld )
+ puts " [sum: " + per_species_counter.to_s + "]"
+ log << " [sum: " + per_species_counter.to_s + "]" + ld
+ end
+
+ def read_fasta_file( input )
+ f = MsaFactory.new()
+ msa = nil
+ begin
+ msa = f.create_msa_from_file( input, FastaParser.new() )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ msa
+ end
+
+ def print_help()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
+ "and possibly genome multiple-sequence ('fasta') files> <output directory> [mapping file for " +
+ "genome multiple-sequence ('fasta') files not in input dir]" )
+ puts()
+ puts( " " + "Example: \"mse.rb .prot . seqs ../genome_locations.txt\"" )
+ puts()
+ end
+
+ end # class MultiSequenceExtractor
+end
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/apps/ - class
+#
+# Copyright:: Copyright (C) 2009 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: new_tap.rb,v 1.4 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/util'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/msa/msa'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/parser/general_msa_parser'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/util/command_line_arguments'
+
+module Evoruby
+
+ class TaxonomyProcessor
+
+ PRG_NAME = ""
+ PRG_DATE = "2009.10.09"
+ PRG_DESC = "replacement of labels in multiple sequence files"
+ PRG_VERSION = "1.00"
+ COPYRIGHT = "2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ REMOVE_REDUNDANT_SEQS_OPTION = "rr"
+
+ def initialize()
+ @taxonomies = Hash.new()
+ end
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 ) )
+ puts( "Usage: #{PRG_NAME}.rb <input sequences> <output sequences> <output map>" )
+ puts()
+ puts( " options: -" + REMOVE_REDUNDANT_SEQS_OPTION + ": to remove redundant sequences" )
+ puts()
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ input = cla.get_file_name( 0 )
+ output = cla.get_file_name( 1 )
+ map_file = cla.get_file_name( 2 )
+
+ allowed_opts = Array.new
+ allowed_opts.push( REMOVE_REDUNDANT_SEQS_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+ end
+
+
+ remove_redudant = false
+ if ( cla.is_option_set?( REMOVE_REDUNDANT_SEQS_OPTION ) )
+ remove_redudant = true
+ end
+
+ if ( File.exists?( output ) )
+ Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" )
+ end
+ if ( File.exists?( map_file ) )
+ Util.fatal_error( PRG_NAME, "map file [" + map_file + "] already exists" )
+ end
+ if ( !File.exists?( input) )
+ Util.fatal_error( PRG_NAME, "infile [" + input + "] does not exist" )
+ end
+
+ fasta_like = Util.looks_like_fasta?( input )
+
+ puts()
+ puts( "Input alignment : " + input )
+ puts( "Output alignment: " + output )
+ puts( "Output map : " + map_file )
+ if ( fasta_like )
+ puts( "Format : Fasta" )
+ else
+ puts( "Format : Phylip like" )
+ end
+ puts()
+
+ species_map = Hash.new
+
+ f = MsaFactory.new()
+ begin
+ if ( fasta_like )
+ msa = f.create_msa_from_file( input, FastaParser.new() )
+ else
+ msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
+ end
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to read file: " + e.to_s )
+ end
+
+ if ( msa == nil || msa.get_number_of_seqs() < 1 )
+ Util.fatal_error( PRG_NAME, "failed to read MSA" )
+ end
+ begin
+ Util.check_file_for_writability( map_file )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_, STDOUT )
+ end
+
+ if ( remove_redudant )
+ removed = msa.remove_redundant_sequences!( true )
+ if removed.size > 0
+ Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
+ removed.each { | seq_name |
+ puts seq_name
+ }
+ Util.print_message( PRG_NAME, "will process " + msa.get_number_of_seqs.to_s + " non redundant sequences" )
+ end
+ end
+
+ lf = File.open( map_file, "a" )
+ for i in 0 ... msa.get_number_of_seqs
+ seq = msa.get_sequence( i )
+ end
+
+ io = MsaIO.new()
+ w = nil
+ if ( fasta_like )
+ w = FastaWriter.new()
+ else
+ w = PhylipSequentialWriter.new()
+ end
+ w.set_max_name_length( 10 )
+ w.clean( true )
+ begin
+ io.write_to_file( msa, output, w )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
+ end
+ lf.close()
+ if ( @taxonomies.length > 0 )
+ Util.print_message( PRG_NAME, "number of unique taxonomies: " + @taxonomies.length.to_s )
+ end
+ Util.print_message( PRG_NAME, "wrote: " + map_file )
+ Util.print_message( PRG_NAME, "wrote: " + output )
+ Util.print_message( PRG_NAME, "OK" )
+ end
+
+ end # class
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = lib/evo/apps/phylogenies_decorator
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# decoration of phylogenies with sequence/species names and domain architectures
+#
+# $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
+#
+# Environment variable FORESTER_HOME needs to point to the appropriate
+# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/)
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+
+require 'date'
+
+module Evoruby
+
+ class PhylogeniesDecorator
+
+ DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
+ # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
+ #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
+ DECORATOR_OPTIONS_DOMAINS = '-r=1'
+ IDS_MAPFILE_SUFFIX = '.nim'
+ DOMAINS_MAPFILE_SUFFIX = '.dff'
+ SLEEP_TIME = 0.1
+ REMOVE_NI = true
+ TMP_FILE = '___PD___'
+ LOG_FILE = '00_phylogenies_decorator.log'
+ FORESTER_HOME = ENV[Constants::FORESTER_HOME_ENV_VARIABLE]
+ JAVA_HOME = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
+
+ PRG_NAME = "phylogenies_decorator"
+ PRG_DATE = "2008.09.02"
+ PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures"
+ PRG_VERSION = "1.0.1"
+ COPYRIGHT = "2008-2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ IDS_ONLY_OPTION = "n"
+ DOMAINS_ONLY_OPTION = "d"
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+ NL = Constants::LINE_DELIMITER
+
+ def run
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ARGV.length > 3 || ARGV.length < 2 )
+ print_help
+ exit( -1 )
+ end
+
+ if FORESTER_HOME == nil || FORESTER_HOME.length < 1
+ Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::FORESTER_HOME_ENV_VARIABLE} has not been set" )
+ end
+ if JAVA_HOME == nil || JAVA_HOME.length < 1
+ Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::JAVA_HOME_ENV_VARIABLE} has not been set" )
+ end
+
+ if !File.exist?( FORESTER_HOME )
+ Util.fatal_error( PRG_NAME, '[' + FORESTER_HOME + '] does not exist' )
+ end
+ if !File.exist?( JAVA_HOME )
+ Util.fatal_error( PRG_NAME, '[' + JAVA_HOME + '] does not exist' )
+ end
+
+ decorator = JAVA_HOME + '/bin/java -cp ' + FORESTER_HOME + '/java/forester.jar org.forester.application.decorator'
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if File.exist?( LOG_FILE )
+ Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( IDS_ONLY_OPTION )
+ allowed_opts.push( DOMAINS_ONLY_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+ end
+
+ ids_only = false
+ domains_only = false
+
+ in_suffix = cla.get_file_name( 0 )
+ out_suffix = cla.get_file_name( 1 )
+
+ if cla.is_option_set?( IDS_ONLY_OPTION )
+ ids_only = true
+ end
+ if cla.is_option_set?( DOMAINS_ONLY_OPTION )
+ domains_only = true
+ end
+
+ if ( ids_only && domains_only )
+ Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' )
+ end
+
+ log = String.new
+
+ now = DateTime.now
+ log << "Program : " + PRG_NAME + NL
+ log << "Version : " + PRG_VERSION + NL
+ log << "Program date : " + PRG_DATE + NL
+ log << "Options for seq names: " + DECORATOR_OPTIONS_SEQ_NAMES + NL
+ log << "Options for domains : " + DECORATOR_OPTIONS_DOMAINS + NL
+ log << "FORESTER_HOME : " + FORESTER_HOME + NL
+ log << "JAVA_HOME : " + JAVA_HOME + NL + NL
+ log << "Date/time: " + now.to_s + NL
+ log << "Directory: " + Dir.getwd + NL + NL
+
+ Util.print_message( PRG_NAME, 'input suffix : ' + in_suffix )
+ Util.print_message( PRG_NAME, 'output suffix : ' + out_suffix )
+
+ log << 'input suffix : ' + in_suffix + NL
+ log << 'output suffix : ' + out_suffix + NL
+
+ if ( File.exists?( TMP_FILE ) )
+ File.delete( TMP_FILE )
+ end
+
+ files = Dir.entries( "." )
+
+ counter = 0
+
+ files.each { | phylogeny_file |
+ if ( !File.directory?( phylogeny_file ) &&
+ phylogeny_file !~ /^\./ &&
+ phylogeny_file !~ /^00/ &&
+ phylogeny_file !~ /#{out_suffix}$/ &&
+ phylogeny_file =~ /#{in_suffix}$/ )
+ begin
+ Util.check_file_for_readability( phylogeny_file )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
+ end
+
+ counter += 1
+
+ outfile = phylogeny_file.sub( /#{in_suffix}$/, out_suffix )
+
+ if REMOVE_NI
+ outfile = outfile.sub( /_ni_/, '_' )
+ end
+
+ if File.exists?( outfile )
+ msg = counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile +
+ ' : already exists, skipping'
+ Util.print_message( PRG_NAME, msg )
+ log << msg + NL
+ next
+ end
+
+ Util.print_message( PRG_NAME, counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile )
+ log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
+
+ phylogeny_id = get_id( phylogeny_file )
+
+ ids_mapfile_name = nil
+ domains_mapfile_name = nil
+
+ if ids_only
+ ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
+ elsif domains_only
+ domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+ else
+ ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
+ domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+ end
+
+ if domains_mapfile_name != nil
+ begin
+ Util.check_file_for_readability( domains_mapfile_name )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
+ end
+ end
+
+ if ids_mapfile_name != nil
+ begin
+ Util.check_file_for_readability( ids_mapfile_name )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
+ end
+ end
+
+ if domains_mapfile_name != nil
+ if ids_mapfile_name != nil
+ my_outfile = TMP_FILE
+ else
+ my_outfile = outfile
+ end
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
+ '-f=d ' + phylogeny_file + ' ' +
+ domains_mapfile_name + ' ' + my_outfile
+ execute_cmd( cmd, log )
+ end
+
+ if ids_mapfile_name != nil
+ if domains_mapfile_name != nil
+ my_infile = TMP_FILE
+ else
+ my_infile = phylogeny_file
+ end
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+ '-f=s ' + my_infile + ' ' +
+ ids_mapfile_name + ' ' + outfile
+ execute_cmd( cmd, log )
+ end
+
+ if ( File.exists?( TMP_FILE ) )
+ File.delete( TMP_FILE )
+ end
+ end
+ }
+ open( LOG_FILE, 'w' ) do | f |
+ f.write( log )
+ end
+ puts
+ Util.print_message( PRG_NAME, 'OK' )
+ puts
+ end # def run
+
+ def execute_cmd( cmd, log )
+ log << 'excuting ' + cmd + NL
+ IO.popen( cmd , 'r+' ) do | pipe |
+ pipe.close_write
+ log << pipe.read + NL + NL
+ end
+ sleep( SLEEP_TIME )
+ end
+
+
+ def get_id( phylogeny_file_name )
+ phylogeny_file_name =~ /^([^_]+)/
+ $1
+ end
+
+ def get_file( files_in_dir, phylogeny_id, suffix_pattern )
+ matching_files = Array.new
+ files_in_dir.each { | file |
+
+ if ( !File.directory?( file ) &&
+ file !~ /^\./ &&
+ file !~ /^00/ &&
+ file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
+ matching_files << file
+ end
+ }
+ if matching_files.length < 1
+ Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
+ '_] [' + suffix_pattern + '] present in current directory' )
+ elsif matching_files.length > 1
+ Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
+ '_] [' + suffix_pattern + '] present in current directory' )
+ end
+ matching_files[ 0 ]
+ end
+
+ def print_help()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
+ puts()
+ puts( " options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
+ puts( " -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures" )
+ puts()
+ end
+ end # class PhylogenyiesDecorator
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/phylogeny_factory - PhylogenyFactory class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: phylogeny_factory.rb,v 1.32 2010/12/13 19:00:11 cmzmasek Exp $
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/util/command_line_arguments'
+
+require 'set'
+require 'date'
+
+module Evoruby
+
+ class PhylogenyFactory
+
+ PRG_NAME = "phylogeny_factory"
+ PRG_DATE = "2010.05.26"
+ PRG_DESC = "automated phylogeny reconstruction using queing system"
+ PRG_VERSION = "1.1"
+ COPYRIGHT = "2010 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ USE_JOB_SUBMISSION_SYSTEM_OPTION = 's'
+ LOG_FILE = '00_phylogeny_factory.log'
+ TEMPLATE_FILE = '00_phylogeny_factory.template'
+ PBS_O_WORKDIR = '$PBS_O_WORKDIR/'
+ MIN_LENGTH_DEFAULT = 40
+ WALLTIME = '100:00:00'
+ QUEUE = 'default'
+
+ TMP_CMD_FILE_SUFFIX = '_QSUB'
+
+ HMM = 'HMM'
+ RSL = 'RSL'
+
+ OPTION_OPEN = '%['
+ OPTION_CLOSE = ']%'
+
+ WAIT = 1.0
+
+ NL = Constants::LINE_DELIMITER
+
+ def run
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( USE_JOB_SUBMISSION_SYSTEM_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME,
+ "unknown option(s): " + disallowed,
+ STDOUT )
+ end
+
+ if File.exists?( LOG_FILE )
+ puts( '[' + PRG_NAME + '] > log file [' + LOG_FILE + '] already exists' )
+ exit( -1 )
+ end
+
+ if !File.exists?( TEMPLATE_FILE )
+ puts( '[' + PRG_NAME + '] > template file [' + TEMPLATE_FILE + '] not found' )
+ exit( -1 )
+ end
+
+ use_job_submission_system = false
+ if cla.is_option_set?( USE_JOB_SUBMISSION_SYSTEM_OPTION )
+ use_job_submission_system = true
+ end
+
+ log = String.new
+
+ now = DateTime.now
+ log << "Program : " + PRG_NAME + NL
+ log << "Version : " + PRG_VERSION + NL
+ log << "Program date: " + PRG_DATE + NL + NL
+ log << "Date/time : " + now.to_s + NL
+ log << "Directory : " + Dir.getwd + NL + NL
+
+ puts( '[' + PRG_NAME + '] > reading ' + TEMPLATE_FILE )
+
+ paths = Hash.new # path placeholder -> full path
+ min_lengths = Hash.new # alignment id -> minimal length
+ hmms = Hash.new # alignment id -> hmm
+ options = Hash.new # option placeholder -> option
+ ids = Set.new
+
+ commands = Array.new
+
+ log << "////////////////////////////////////////////////////////////////// #{NL}"
+ log << "Template file [" + TEMPLATE_FILE + "]:#{NL}"
+
+ command = String.new
+
+ open( TEMPLATE_FILE ).each { | line |
+ log << line
+ if ( line =~ /^#/ )
+ elsif ( line =~ /^\$\s*(\S+)\s*=\s*(\S+)/ )
+ paths[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > paths : ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^%\s*#{HMM}\s*(\S+)\s*=\s*(\S+)/ )
+ hmms[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > hmms : ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^%\s*#{RSL}\s*(\S+)\s*=\s*(\S+)/ )
+ min_lengths[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > min lengths: ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ )
+ options[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > options : ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^>\s*(.+)/ )
+ command = command + $1 + ";#{NL}"
+
+ elsif ( line =~ /^-/ )
+ commands << prepare( command, paths )
+ command = String.new
+ end
+ }
+ log << "\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ #{NL}#{NL}"
+
+ files = Dir.entries( "." )
+
+ files.each { | file |
+ if ( !File.directory?( file ) &&
+ file !~ /^\./ &&
+ file !~ /#{TEMPLATE_FILE}/ &&
+ file !~ /.bck$/ &&
+ file !~ /.log$/ &&
+ file !~ /nohup/ &&
+ file !~ /^00/ )
+ aln_name = file.to_str
+ id = get_id( aln_name )
+ if !ids.include?( id )
+ ids.add( id )
+ end
+ puts( '[' + PRG_NAME + '] > file [id] : ' + aln_name + ' [' + id + ']' )
+ commands.each do | cmd |
+
+ cmd = subst_hmm( cmd, aln_name, hmms )
+ cmd = subst_min_length( cmd, aln_name, min_lengths )
+ cmd = subst_options( cmd, options )
+ if use_job_submission_system
+ cmd = subst_aln_name( cmd, PBS_O_WORKDIR + aln_name )
+ else
+ cmd = subst_aln_name( cmd, aln_name )
+ end
+
+ if ( cmd =~ /%/ )
+ cmd =~ /(%.*?%)/
+ problem = $1
+ puts( '[' + PRG_NAME + '] > WARNING : [' + id + '] command still contains placeholder: ' + problem )
+ log << "WARNING: command still contains placeholder: " + cmd + NL
+ else
+ tmp_cmd_file = file.to_str[ 0..4 ] + TMP_CMD_FILE_SUFFIX
+ if ( File.exists?( tmp_cmd_file ) )
+ File.delete( tmp_cmd_file )
+ end
+ if use_job_submission_system
+ open( tmp_cmd_file, 'w' ) do |f|
+ f.write( cmd )
+ end
+ end
+
+ log << cmd + NL
+
+ if use_job_submission_system
+ IO.popen( 'qsub -q ' + QUEUE + ' -l walltime=' + WALLTIME + ' ' + tmp_cmd_file , 'r+' ) do | pipe |
+ pipe.close_write
+ end
+ else
+ spawn( 'nohup ' + cmd + ' &', STDERR => "/dev/null" )
+ end
+
+ sleep( WAIT )
+ if ( File.exists?( tmp_cmd_file ) )
+ File.delete( tmp_cmd_file )
+ end
+ end
+ end
+ end
+ }
+
+ open( LOG_FILE, 'w' ) do | f |
+ f.write( log )
+ end
+
+ puts()
+ puts( '[' + PRG_NAME + '] > OK' )
+ puts()
+
+ end # def run
+
+ def prepare( command, paths )
+ paths.each_pair{ | name, full |
+ command = command.gsub( name, full )
+ }
+ command
+ end
+
+ def subst_options( command, options )
+ opt_placeholders = command.scan( /%\[\S+\]%/ )
+ opt_placeholders.each { | opt_placeholder |
+ opt_placeholder = opt_placeholder.gsub( OPTION_OPEN , '' )
+ opt_placeholder = opt_placeholder.gsub( OPTION_CLOSE, '' )
+ opt_value = options[ opt_placeholder ]
+ if ( opt_value != nil && opt_value.size > 0 )
+ command = command.gsub( OPTION_OPEN + opt_placeholder + OPTION_CLOSE, opt_value )
+ end
+ }
+ command
+ end
+
+ def subst_aln_name( command, aln_name )
+ command = command.gsub( '$', aln_name )
+ command
+ end
+
+ def subst_hmm( command, aln_name, hmms )
+ id = get_id( aln_name )
+ hmm = hmms[ id ]
+ if ( hmm != nil && hmm.size > 0 )
+ command = command.gsub( OPTION_OPEN + HMM + OPTION_CLOSE, hmm )
+ end
+ command
+ end
+
+ def subst_min_length( command, aln_name, min_lengths )
+ id = get_id( aln_name )
+ min_length = min_lengths[ id ]
+ if ( min_length != nil && min_length.size > 0 )
+ command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, min_length )
+ else
+ command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, MIN_LENGTH_DEFAULT.to_s )
+ end
+ command
+ end
+
+ def get_id( aln_name )
+ aln_name =~ /^([^_]+)/
+ $1
+ end
+
+ end # class PhylogenyFactory
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/taxonomy_processor - TaxonomyProcessor class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: taxonomy_processor.rb,v 1.26 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/util'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/msa/msa'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/parser/general_msa_parser'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/util/command_line_arguments'
+
+module Evoruby
+
+ class TaxonomyProcessor
+
+ PRG_NAME = "tap"
+ PRG_DATE = "2010.02.24"
+ PRG_DESC = "replacement of species names in multiple sequence files"
+ PRG_VERSION = "1.01"
+ COPYRIGHT = "2010 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ EXTRACT_TAXONOMY_OPTION = "t"
+
+ def initialize()
+ @taxonomies = Hash.new()
+ end
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 && ARGV.length != 5 && ARGV.length != 6 ) )
+ puts( "Usage: #{PRG_NAME}.rb [options] [input map file] <input sequences> <output sequences> <output id list>" )
+ puts()
+ puts( " options: -" + EXTRACT_TAXONOMY_OPTION + ": to extract taxonomy information from bracketed expression" )
+ puts()
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ mapfile = nil
+ input = nil
+ output = nil
+ list_file = nil
+
+ if cla.get_number_of_files == 4
+ mapfile = cla.get_file_name( 0 )
+ input = cla.get_file_name( 1 )
+ output = cla.get_file_name( 2 )
+ list_file = cla.get_file_name( 3 )
+ elsif cla.get_number_of_files == 3
+ input = cla.get_file_name( 0 )
+ output = cla.get_file_name( 1 )
+ list_file = cla.get_file_name( 2 )
+ end
+
+
+ allowed_opts = Array.new
+ allowed_opts.push( EXTRACT_TAXONOMY_OPTION )
+
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+ end
+
+ extract_taxonomy = false
+ if ( cla.is_option_set?( EXTRACT_TAXONOMY_OPTION ) )
+ extract_taxonomy = true
+ end
+
+ if ( File.exists?( output ) )
+ Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" )
+ end
+ if ( File.exists?( list_file ) )
+ Util.fatal_error( PRG_NAME, "list file [" + list_file + "] already exists" )
+ end
+ if ( !File.exists?( input) )
+ Util.fatal_error( PRG_NAME, "infile [" + input + "] does not exist" )
+ end
+ if ( mapfile != nil && !File.exists?( mapfile ) )
+ Util.fatal_error( PRG_NAME, "mapfile [" + mapfile + "] does not exist" )
+ end
+
+ fasta_like = Util.looks_like_fasta?( input )
+
+ puts()
+ if mapfile != nil
+ puts( "Map file : " + mapfile )
+ end
+ puts( "Input alignment : " + input )
+ puts( "Output alignment: " + output )
+ puts( "Name list : " + list_file )
+ if ( fasta_like )
+ puts( "Format : Fasta" )
+ else
+ puts( "Format : Phylip like" )
+ end
+ if ( extract_taxonomy )
+ puts( "Extract taxonomy: true" )
+ end
+ puts()
+
+ species_map = Hash.new
+ if mapfile != nil
+ File.open( mapfile ) do | file |
+ while line = file.gets
+ if ( line =~/(.+)#(.+)/ || line =~/(.+)\s+(.+)/ )
+ species_map[ $1 ] = $2
+ Util.print_message( PRG_NAME, "mapping: " + $1 + ' => ' + $2 )
+ end
+ end
+ end
+ end
+
+ f = MsaFactory.new()
+ begin
+ if ( fasta_like )
+ msa = f.create_msa_from_file( input, FastaParser.new() )
+ else
+ msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
+ end
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to read file: " + e.to_s )
+ end
+
+ if ( msa == nil || msa.get_number_of_seqs() < 1 )
+ Util.fatal_error( PRG_NAME, "failed to read MSA" )
+ end
+ begin
+ Util.check_file_for_writability( list_file )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_, STDOUT )
+ end
+
+ #removed = msa.remove_redundant_sequences!( true )
+ #if removed.size > 0
+ # Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
+ # removed.each { | seq_name |
+ # puts seq_name
+ # }
+ # Util.print_message( PRG_NAME, "will process " + msa.get_number_of_seqs.to_s + " non redundant sequences" )
+ #end
+
+ lf = File.open( list_file, "a" )
+ for i in 0 ... msa.get_number_of_seqs
+ seq = msa.get_sequence( i )
+ seq.set_name( Util::normalize_seq_name( modify_name( seq.get_name(), i, lf, species_map, extract_taxonomy ), 10 ) )
+ end
+
+ io = MsaIO.new()
+ w = nil
+ if ( fasta_like )
+ w = FastaWriter.new()
+ else
+ w = PhylipSequentialWriter.new()
+ end
+ w.set_max_name_length( 10 )
+ w.clean( true )
+ begin
+ io.write_to_file( msa, output, w )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
+ end
+ lf.close()
+ if ( @taxonomies.length > 0 )
+ Util.print_message( PRG_NAME, "number of unique taxonomies: " + @taxonomies.length.to_s )
+ end
+ Util.print_message( PRG_NAME, "wrote: " + list_file )
+ Util.print_message( PRG_NAME, "wrote: " + output )
+ Util.print_message( PRG_NAME, "OK" )
+ end
+
+ private
+
+ def modify_name( desc, counter, file, species_map, extract_taxonomy )
+ new_desc = nil
+ my_species = nil
+ if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/
+ new_desc = counter.to_s( 16 ) + "_" + $1
+ elsif extract_taxonomy
+ if ( desc.count( "[" ) != desc.count( "]" ) )
+ Util.fatal_error( PRG_NAME, "illegal bracket count in: " + desc )
+ end
+ species = nil
+ species_map.each_key do | key |
+ if desc =~ /[\b|_]#{key}\b/ # Added boundaries to prevent e.g. RAT matching ARATH.
+ species = species_map[ key ]
+ new_desc = counter.to_s( 16 ) + "_" + species
+ break
+ end
+ end
+ if species == nil
+ if desc =~/.*\[(\S{3,}?)\]/
+ species = $1
+ species.strip!
+ species.upcase!
+ species.gsub!( /\s+/, " " )
+ species.gsub!( /-/, "" )
+ species.gsub!( /\)/, "" )
+ species.gsub!( /\(/, "" )
+ species.gsub!( /\'/, "" )
+ if species =~ /\S+\s\S+/ || species =~ /\S{3,5}/
+ if species =~ /(\S+)\s(\S+)/
+ code = $1[ 0..2 ] + $2[ 0..1 ]
+ elsif species =~ /\S{3,5}/
+ code = species
+ elsif species.count( " " ) > 2
+ species =~ /(\S+)\s+(\S+)\s+(\S+)$/
+ third_last = $1
+ second_last = $2
+ last = $3
+ code = code[ 0 ] + third_last[ 0 ] + second_last[ 0 ] + last[ 0 ] + last[ last.size - 1 ]
+ elsif species.count( " " ) > 1
+ species =~ /(\S+)\s+(\S+)$/
+ second_last = $1
+ last = $2
+ code = code[ 0..1 ] + second_last[ 0 ] + last[ 0 ] + last[ last.size - 1 ]
+ end
+ new_desc = counter.to_s( 16 ) + "_" + code
+ if @taxonomies.has_key?( code )
+ if ( !@taxonomies.has_value?( species ) )
+ Util.fatal_error( PRG_NAME, "code [#{code}] is not unique in [#{desc}]" )
+ end
+ else
+ if ( @taxonomies.has_value?( species ) )
+ Util.fatal_error( PRG_NAME, "genome [#{species}] is not unique in [#{desc}]" )
+ else
+ @taxonomies[ code ] = species
+ end
+ end
+ else
+ Util.fatal_error( PRG_NAME, "illegal format [#{species}] in: " + desc )
+ end
+ else
+ Util.fatal_error( PRG_NAME, "illegal format in: " + desc )
+ end
+ end
+ else
+ species = nil
+ my_species = nil
+ species_map.each_key do | key |
+ if desc =~ /#{key}/
+ species = species_map[ key ]
+ species = species.gsub( /\s+/, "" )
+ species = species.gsub( /_/, " " )
+ my_species = species
+ if species =~ /(\S+)\s+(\S+)/
+ species = $1[0..2] + $2[0..1]
+ end
+ species = species.gsub( /\s+/, "" )
+ species = species.slice(0, 5)
+ species.upcase!
+ break
+ end
+ end
+ if species == nil
+ Util.fatal_error( PRG_NAME, "species not found in: " + desc )
+ else
+ new_desc = counter.to_s( 16 ) + "_" + species
+ end
+ end
+ if new_desc == nil
+ Util.fatal_error( PRG_NAME, "failed to extract species from: " + desc )
+ end
+ if my_species != nil
+ file.print( new_desc + ": " + desc + " [" + my_species + "]" + "\n" )
+ else
+ file.print( new_desc + ": " + desc + "\n" )
+ end
+ new_desc
+ end
+
+ end # class TaxonomyProcessor
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/apps/tseq_taxonomy_processor - TseqTaxonomyProcessor class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: tseq_taxonomy_processor.rb,v 1.6 2010/12/13 19:00:11 cmzmasek Exp $
+
+
+require 'lib/evo/util/util'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/msa/msa'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/parser/sp_taxonomy_parser'
+require 'lib/evo/io/parser/ncbi_tseq_parser'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/writer/phylip_sequential_writer'
+require 'lib/evo/util/command_line_arguments'
+
+module Evoruby
+
+ class TseqTaxonomyProcessor
+
+ PRG_NAME = "tseq_tap"
+ PRG_DATE = "2009.01.06"
+ PRG_DESC = "preprocessing of multiple sequence files in ncbi tseq xml format"
+ PRG_VERSION = "1.02"
+ COPYRIGHT = "2009 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ TAXONOMY_CODE = "TAXONOMY_CODE:"
+ TAXONOMY_ID = "TAXONOMY_ID:"
+ TAXONOMY_ID_TYPE = "TAXONOMY_ID_TYPE:"
+ TAXONOMY_SN = "TAXONOMY_SN:"
+ TAXONOMY_CN = "TAXONOMY_CN:"
+ SEQ_ACCESSION = "SEQ_ACCESSION:"
+ SEQ_ACCESSION_SOURCE = "SEQ_ACCESSION_SOURCE:"
+ SEQ_SECONDARY_ACCESSION = "SEQ_SECONDARY_ACCESSION:"
+ SEQ_SYMBOL = "SEQ_SYMBOL:"
+ SEQ_NAME = "SEQ_NAME:"
+ SEQ_MOL_SEQ = "SEQ_MOL_SEQ:"
+
+ def initialize()
+ @tax_ids_to_sp_taxonomies = Hash.new()
+ end
+
+ def run()
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ if ARGV == nil || ARGV.length != 4
+ puts( "Usage: #{PRG_NAME}.rb <sp taxonomy file> <sequences in tseq xml format> <name for fasta outfile> <name for map outfile>" )
+ puts()
+
+ exit( -1 )
+ end
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ allowed_opts = Array.new
+ disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+ if ( disallowed.length > 0 )
+ Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+ end
+
+ sp_taxonomy_infile = cla.get_file_name( 0 )
+ sequences_infile = cla.get_file_name( 1 )
+ sequences_outfile = cla.get_file_name( 2 )
+ mapping_outfile = cla.get_file_name( 3 )
+
+ Util.fatal_error_if_not_readable( PRG_NAME, sp_taxonomy_infile )
+ Util.fatal_error_if_not_readable( PRG_NAME, sequences_infile )
+ Util.fatal_error_if_not_writable( PRG_NAME, mapping_outfile )
+ Util.fatal_error_if_not_writable( PRG_NAME, sequences_outfile )
+
+ sp_taxonomies = SpTaxonomyParser.parse( sp_taxonomy_infile )
+
+ Util.print_message( PRG_NAME, "read in taxonomic data for " + sp_taxonomies.size.to_s + " species from: " + sp_taxonomy_infile )
+
+ tseq_parser = NcbiTSeqParser.new
+ msa_fac = MsaFactory.new
+
+ seqs = msa_fac.create_msa_from_file( sequences_infile, tseq_parser )
+
+ Util.print_message( PRG_NAME, "read in " + seqs.get_number_of_seqs.to_s + " sequences from: " + sequences_infile )
+
+ removed = seqs.remove_redundant_sequences!( true, true )
+
+ if removed.size > 0
+ Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
+ removed.each { | seq_name |
+ puts seq_name
+ }
+ Util.print_message( PRG_NAME, "will process " + seqs.get_number_of_seqs.to_s + " non-redundant sequences" )
+ end
+
+ mapping_out = File.open( mapping_outfile, "a" )
+
+ for i in 0 ... seqs.get_number_of_seqs
+ seq = seqs.get_sequence( i )
+ if seq.get_taxonomy == nil
+ Util.fatal_error( PRG_NAME, "sequence [" + seq.get_name + "] has no taxonomy information" )
+ end
+ seq.set_name( Util::normalize_seq_name( modify_name( seq, i, sp_taxonomies, mapping_out ), 10 ) )
+ end
+
+ io = MsaIO.new()
+
+ w = FastaWriter.new()
+
+ w.set_max_name_length( 10 )
+ w.clean( true )
+ begin
+ io.write_to_file( seqs, sequences_outfile, w )
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
+ end
+ mapping_out.close()
+
+ Util.print_message( PRG_NAME, "wrote: " + mapping_outfile )
+ Util.print_message( PRG_NAME, "wrote: " + sequences_outfile )
+ Util.print_message( PRG_NAME, "OK" )
+
+ end
+
+ private
+
+ def modify_name( seq, i, sp_taxonomies, mapping_outfile )
+
+ tax_id = seq.get_taxonomy.get_id
+ matching_sp_taxonomy = nil
+
+ if @tax_ids_to_sp_taxonomies.has_key?( tax_id )
+ # This is so that a second lookup will be much faster.
+ matching_sp_taxonomy = @tax_ids_to_sp_taxonomies[ tax_id ]
+ else
+ sp_taxonomies.each { |sp_taxonomy|
+ if ( sp_taxonomy.id == tax_id )
+ if matching_sp_taxonomy != nil
+ Util.fatal_error( PRG_NAME, "taxonomy id [" + tax_id.to_s + "] is not unique" )
+ end
+ matching_sp_taxonomy = sp_taxonomy
+ @tax_ids_to_sp_taxonomies[ tax_id ] = sp_taxonomy
+ end
+ }
+ end
+ if matching_sp_taxonomy == nil
+ Util.fatal_error( PRG_NAME, "taxonomy id [" + tax_id.to_s + "] for [" + seq.get_taxonomy.get_name + "] not found" )
+ end
+
+ new_name = i.to_s( 16 ) + "_" + matching_sp_taxonomy.code
+
+ seq_name = seq.get_name
+ if seq_name =~ /\[.+\]$/
+ # Redundant taxonomy information hides here.
+ seq_name = seq_name.sub(/\[.+\]$/, '')
+ end
+ if seq_name =~ /^\s*hypothetical\s+protein\s*/i
+ # Pointless information.
+ seq_name = seq_name.sub( /^\s*hypothetical\s+protein\s*/i, '' )
+ end
+
+ mapping_outfile.print( new_name + "\t" +
+ TAXONOMY_CODE + matching_sp_taxonomy.code + "\t" +
+ TAXONOMY_ID + tax_id + "\t" +
+ TAXONOMY_ID_TYPE + seq.get_taxonomy.get_id_source + "\t" +
+ TAXONOMY_SN + matching_sp_taxonomy.scientific_name + "\t" +
+ SEQ_ACCESSION + seq.get_accession + "\t" +
+ SEQ_ACCESSION_SOURCE + seq.get_accession_source + "\t" +
+ SEQ_SYMBOL + seq.get_symbol + "\t" +
+ SEQ_NAME + seq_name + "\t" +
+ SEQ_MOL_SEQ + seq.get_sequence_as_string +
+ Constants::LINE_DELIMITER )
+ new_name
+ end
+
+ end
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/io/msa_io.rb - MsaIO class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_io.rb,v 1.2 2007/06/12 04:51:35 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class MsaIO
+
+ def initialize()
+ end
+
+ def write_to_file( msa, path, msa_writer )
+ msa_writer.write( msa, path )
+ end
+
+ end # module Evoruby
+
+end # class MsaIO
--- /dev/null
+#
+# = lib/evo/io/parser/basic_table_parser - BasicTableParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: basic_table_parser.rb,v 1.3 2007/09/28 03:12:10 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class BasicTableParser
+
+ START_OF_COMMENT_LINE_CHAR = "#"
+
+ # raises ArgumentError
+ def BasicTableParser.parse( path, column_delimiter )
+ Util.check_file_for_readability( path )
+ table = BasicTable.new
+ row = 0
+ File.open( path ) do | file |
+ while line = file.gets
+ if ( !Util.is_string_empty?( line ) &&
+ !line.slice( 0, 1 ).eql?( START_OF_COMMENT_LINE_CHAR ) )
+ values = line.split( column_delimiter )
+ col = 0
+ values.each { | value |
+ table.set_value( row, col, value.strip! )
+ col += 1
+ }
+ row += 1
+ end
+ end
+ end
+ return table
+ end
+
+ end # class BasicTableParser
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/parser/fasta_parser - FastaParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fasta_parser.rb,v 1.11 2010/10/08 22:04:17 cmzmasek Exp $
+#
+# last modified: 05/17/2007
+
+require 'lib/evo/io/parser/msa_parser'
+require 'lib/evo/msa/msa'
+
+require 'iconv'
+
+module Evoruby
+
+ class FastaParser < MsaParser
+
+ def initialize
+ end
+
+ def parse( path )
+ Util.check_file_for_readability( path )
+ msa = Msa.new
+ current_seq = String.new()
+ name = String.new()
+ saw_first_seq = false
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+ File.open( path ) do | file |
+ while line = file.gets
+ line = ic.iconv( line )
+ if can_ignore?( line, saw_first_seq )
+
+ elsif line =~ /^\s*>\s*(.+)/
+ saw_first_seq = true
+ add_seq( name, current_seq, msa )
+ name = $1
+ current_seq = String.new()
+ elsif line =~ /^\s*(.+)/
+ if name.length < 1
+ error_msg = "format error at: " + line
+ raise IOError, error_msg
+ end
+ # was: seq = $1.rstrip
+ seq = $1.gsub(/\s+/, '')
+ current_seq = current_seq + seq
+ else
+ error_msg = "Unexpected line: " + line
+ raise IOError, error_msg
+ end
+ end
+ end
+ add_seq( name, current_seq, msa )
+ return msa
+ end
+
+ private
+
+ def add_seq( name, seq, msa )
+ if name.length > 0 && seq.length > 0
+ msa.add( name, seq )
+ end
+ end
+
+ def can_ignore?( line, saw_first_seq )
+ return ( line !~ /\S/ ||
+ line =~ /^\s*#/ ||
+ line =~ /^\s*%/ ||
+ line =~ /^\s*\/\// ||
+ line =~ /^\s*!!/ ||
+ ( !saw_first_seq && line =~/^\s*[^>]/ ) )
+ end
+
+ end # class FastaParser
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/parser/general_msa_parser - GeneralMsaParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: general_msa_parser.rb,v 1.8 2009/10/08 22:44:54 cmzmasek Exp $
+#
+# last modified: 2009/10/08
+
+require 'lib/evo/io/parser/msa_parser'
+require 'lib/evo/msa/msa'
+
+require 'iconv'
+
+module Evoruby
+
+ class GeneralMsaParser < MsaParser
+
+ def initialize
+ end
+
+ def parse( path )
+ Util.check_file_for_readability( path )
+ block = -1
+ current_seq_index_per_block = -1
+ current_name = nil
+ saw_ignorable = true
+ is_first = true
+ msa = Msa.new
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+ File.open( path ) do | file |
+ while line = file.gets
+ line = ic.iconv( line )
+ if can_ignore?( line )
+ saw_ignorable = true
+ elsif ( is_first && is_program_name_line?( line ) )
+ elsif( line =~ /^\S+\s+.+\s*$/ || line =~ /^\s+.+\s*$/ || line =~ /^\S+\s*$/ )
+ if ( saw_ignorable )
+ block += 1
+ current_seq_index_per_block = -1
+ saw_ignorable = false
+ end
+ current_seq_index_per_block += 1
+ if ( line =~ /^(\S+)\s+(.+?)\s*$/ )
+ name = $1
+ seq = $2.gsub( /\s/, '.' )
+ a = msa.find_by_name( name, false, false )
+ if ( a.length < 1 )
+ msa.add( name, seq )
+ elsif ( a.length == 1 )
+ msa.get_sequence( a[ 0 ] ).append!( seq )
+ else
+ error_msg = "Unexpected error at line: " + line
+ raise IOError, error_msg
+ end
+ current_name = name
+ elsif ( line =~ /^\s+(.+?)\s*$/ )
+ seq = $1.gsub( /\s/, '.' )
+ a = msa.find_by_name( current_name, false, false )
+ if ( a.length != 1 )
+ error_msg = "Unexpected error at line: " + line
+ raise IOError, error_msg
+ else
+ msa.get_sequence( a[ 0 ] ).append!( seq )
+ end
+
+ elsif ( line =~ /^(\S+)\s*$/ )
+ seq = $1
+ if block == 0
+ error_msg = "First block cannot contain unnamed sequences"
+ raise IOError, error_msg
+ else
+ msa.get_sequence( current_seq_index_per_block ).append!( seq )
+ end
+ current_name = nil
+ end
+ else
+ error_msg = "Unexpected line: " + line
+ raise IOError, error_msg
+ end
+ if ( is_first )
+ is_first = false
+ end
+ end
+ end
+ return msa
+ end # def parse( path )
+
+ private
+
+ def can_ignore?( line )
+ return ( line !~ /[A-Za-z\-?\*_\.]/ ||
+ line =~ /^\s+[*\.:]/ ||
+ line =~ /^\s*#/ ||
+ line =~ /^\s*%/ ||
+ line =~ /^\s*\/\// ||
+ line =~ /^\s*!!/ )
+ end
+
+ def is_program_name_line?( line )
+ return ( line =~ /^CLUSTAL\s/ ||
+ line =~ /^MUSCLE\s\(/ ||
+ line =~ /^PROBCONS\s/ )
+ end
+ end # class GeneralMsaParser
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/parser/hmmsearch_domain_extractor.rb - HmmsearchDomainExtractor class
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: hmmsearch_domain_extractor.rb,v 1.24 2009/11/25 06:30:24 cmzmasek Exp $
+
+
+require 'lib/evo/util/constants'
+require 'lib/evo/msa/msa_factory'
+require 'lib/evo/io/msa_io'
+require 'lib/evo/io/writer/fasta_writer'
+require 'lib/evo/io/parser/fasta_parser'
+
+
+module Evoruby
+
+ class HmmsearchDomainExtractor
+
+ TRIM_BY = 2
+
+ def initialize
+ end
+
+ # raises ArgumentError, IOError, StandardError
+ def parse( hmmsearch_output,
+ fasta_sequence_file,
+ outfile,
+ passed_seqs_outfile,
+ failed_seqs_outfile,
+ e_value_threshold,
+ length_threshold,
+ add_position,
+ add_domain_number,
+ add_domain_number_as_digit,
+ add_domain_number_as_letter,
+ trim_name,
+ log )
+
+ Util.check_file_for_readability( hmmsearch_output )
+ Util.check_file_for_readability( fasta_sequence_file )
+ Util.check_file_for_writability( outfile )
+ Util.check_file_for_writability( passed_seqs_outfile )
+ Util.check_file_for_writability( failed_seqs_outfile )
+
+ in_msa = nil
+ factory = MsaFactory.new()
+ in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
+
+ if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
+ error_msg = "could not find fasta sequences in " + fasta_sequence_file
+ raise IOError, error_msg
+ end
+
+ out_msa = Msa.new
+ failed_seqs = Msa.new
+ passed_seqs = Msa.new
+
+ ld = Constants::LINE_DELIMITER
+
+ domain_pass_counter = 0
+ domain_fail_counter = 0
+ proteins_with_passing_domains = 0
+ proteins_with_failing_domains = 0
+ max_domain_copy_number_per_protein = -1
+ max_domain_copy_number_sequence = ''
+ failed_species_counts = Hash.new
+ passed_species_counts = Hash.new
+
+ File.open( hmmsearch_output ) do | file |
+ while line = file.gets
+ if !is_ignorable?( line ) && line =~ /^\S+\s+/
+
+ # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
+ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
+ line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/
+
+ # line =~ /^(\S+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)/
+ sequence = $1
+ number = $10.to_i
+ out_of = $11.to_i
+ env_from = $20.to_i
+ env_to = $21.to_i
+ i_e_value = $13.to_f
+ if ( number > max_domain_copy_number_per_protein )
+ max_domain_copy_number_sequence = sequence
+ max_domain_copy_number_per_protein = number
+ end
+ if ( ( ( e_value_threshold.to_f < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
+ ( ( length_threshold.to_f <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
+ HmmsearchDomainExtractor.extract_domain( sequence,
+ number,
+ out_of,
+ env_from,
+ env_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ add_domain_number_as_digit,
+ add_domain_number_as_letter,
+ trim_name )
+ domain_pass_counter += 1
+ count_species( sequence, passed_species_counts )
+ if !passed_seqs.has?( sequence, true, false )
+ HmmsearchDomainExtractor.add_sequence( sequence, in_msa, passed_seqs )
+ proteins_with_passing_domains += 1
+ end
+ else
+ print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
+ log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
+ if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
+ print( " iE=" + i_e_value.to_s )
+ log << " iE=" + i_e_value.to_s
+ end
+ if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
+ le = env_to - env_from + 1
+ print( " l=" + le.to_s )
+ log << " l=" + le.to_s
+ end
+ print( Constants::LINE_DELIMITER )
+ log << Constants::LINE_DELIMITER
+ domain_fail_counter += 1
+ count_species( sequence, failed_species_counts )
+ if !failed_seqs.has?( sequence, true, false )
+ HmmsearchDomainExtractor.add_sequence( sequence, in_msa, failed_seqs )
+ proteins_with_failing_domains += 1
+ end
+ end
+ end
+ end
+ end
+
+ if domain_pass_counter < 1
+ error_msg = "no domain sequences were extracted"
+ raise StandardError, error_msg
+ end
+
+ log << Constants::LINE_DELIMITER
+ puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
+ log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
+ log << Constants::LINE_DELIMITER
+
+ if ( max_domain_copy_number_per_protein > 1 )
+ puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
+ log << "First protein with this copy number: " + max_domain_copy_number_sequence
+ log << Constants::LINE_DELIMITER
+ end
+
+ io = MsaIO.new()
+ w = FastaWriter.new()
+ w.set_line_width( 60 )
+ w.clean( true )
+
+ begin
+ io.write_to_file( out_msa, outfile, w )
+ rescue Exception
+ error_msg = "could not write to \"" + outfile + "\""
+ raise IOError, error_msg
+ end
+
+ begin
+ io.write_to_file( passed_seqs, passed_seqs_outfile, w )
+ rescue Exception
+ error_msg = "could not write to \"" + passed_seqs_outfile + "\""
+ raise IOError, error_msg
+ end
+
+ begin
+ io.write_to_file( failed_seqs, failed_seqs_outfile, w )
+ rescue Exception
+ error_msg = "could not write to \"" + failed_seqs_outfile + "\""
+ raise IOError, error_msg
+ end
+
+ log << ld
+ log << "passing domains : " + domain_pass_counter.to_s + ld
+ log << "failing domains : " + domain_fail_counter.to_s + ld
+ log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld
+ log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
+ log << ld
+ log << 'passing domains counts per species: ' << ld
+ passed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
+ log << ld
+ log << 'failing domains counts per species: ' << ld
+ failed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
+ log << ld
+ return domain_pass_counter
+
+ end # parse
+
+ private
+
+
+ def HmmsearchDomainExtractor.add_sequence( sequence_name, in_msa, add_to_msa )
+ seqs = in_msa.find_by_name( sequence_name, true, false )
+ if ( seqs.length < 1 )
+ error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
+ raise StandardError, error_msg
+ end
+ if ( seqs.length > 1 )
+ error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
+ raise StandardError, error_msg
+ end
+ seq = in_msa.get_sequence( seqs[ 0 ] )
+ add_to_msa.add_sequence( seq )
+ end
+
+ # raises ArgumentError, StandardError
+ def HmmsearchDomainExtractor.extract_domain( sequence,
+ number,
+ out_of,
+ seq_from,
+ seq_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ add_domain_number_as_digit,
+ add_domain_number_as_letter,
+ trim_name )
+ if ( number < 1 || out_of < 1 || number > out_of )
+ error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
+ raise ArgumentError, error_msg
+ end
+ if ( seq_from < 1 || seq_to < 1 || seq_from >= seq_to )
+ error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
+ raise ArgumentError, error_msg
+ end
+ seqs = in_msa.find_by_name( sequence, true, false )
+ if ( seqs.length < 1 )
+ error_msg = "sequence \"" + sequence + "\" not found in sequence file"
+ raise StandardError, error_msg
+ end
+ if ( seqs.length > 1 )
+ error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
+ raise StandardError, error_msg
+ end
+ # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
+ seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
+ if ( add_position )
+ seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
+ end
+
+ if ( trim_name )
+ seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] )
+ end
+
+ if ( out_of != 1 )
+ if ( add_domain_number_as_digit )
+ seq.set_name( seq.get_name + number.to_s )
+ elsif ( add_domain_number_as_letter )
+ if number > 25
+ error_msg = 'too many identical domains per sequence, cannot use letters to distinguish them'
+ raise StandardError, error_msg
+ end
+ seq.set_name( seq.get_name + ( number + 96 ).chr )
+ elsif ( add_domain_number )
+ seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
+ end
+ end
+
+ if ( seq.get_name.length > 10 )
+ error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters"
+ raise StandardError, error_msg
+ end
+
+ out_msa.add_sequence( seq )
+ end
+
+ def count_species( sequence, species_counts_map )
+ species = get_species( sequence )
+ if species != nil
+ if !species_counts_map.has_key?( species )
+ species_counts_map[ species ] = 1
+ else
+ species_counts_map[ species ] = species_counts_map[ species ] + 1
+ end
+ end
+ end
+
+ def get_species( sequence_name )
+ if sequence_name =~ /^.+_(.+)$/
+ return $1
+ else
+ return nil
+ end
+ end
+
+ def is_ignorable?( line )
+ return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
+ end
+
+ end # class HmmsearchDomainExtractor
+
+end # module Evoruby
+
--- /dev/null
+#
+# = lib/evo/io/parser/msa_parser - MsaParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_parser.rb,v 1.2 2007/06/12 04:51:34 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class MsaParser
+ def initialize()
+ raise TypeError, "Cannot instanciate abstract class MsaParser"
+ end
+
+ def parse( path )
+ end
+ end
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/parser/ncbi_tseq_parser - NcbiTSeqParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: ncbi_tseq_parser.rb,v 1.5 2009/01/07 02:48:20 cmzmasek Exp $
+
+
+require 'lib/evo/io/parser/msa_parser'
+require 'lib/evo/taxonomy/taxonomy'
+require 'lib/evo/msa/msa'
+
+require 'iconv'
+
+module Evoruby
+
+ class NcbiTSeqParser < MsaParser
+
+ TSEQ_SEQ = "TSeq_sequence"
+ TSEQ_DEFLINE = "TSeq_defline"
+ TSEQ_ORGNAME = "TSeq_orgname"
+ TSEQ_TAXID = "TSeq_taxid"
+ TSEQ_SID = "TSeq_sid"
+ TSEQ_ACCVER = "TSeq_accver"
+ TSEQ_GI = "TSeq_gi"
+ TSEQ_TYPE = "TSeq_seqtype"
+ TSEQ_LENGTH = "TSeq_length"
+
+ def initialize
+ end
+
+
+ # <TSeqSet>
+ #<TSeq>
+ # <TSeq_seqtype value="protein"/>
+ # <TSeq_gi>29341016</TSeq_gi>
+ # <TSeq_accver>AAO78806.1</TSeq_accver>
+ # <TSeq_sid>gnl|mbpwusl|BT3701</TSeq_sid>
+ # <TSeq_taxid>226186</TSeq_taxid>
+ # <TSeq_orgname>Bacteroides thetaiotaomicron VPI-5482</TSeq_orgname>
+ # <TSeq_defline>SusD [Bacteroides thetaiotaomicron VPI-5482]</TSeq_defline>
+ # <TSeq_length>551</TSeq_length>
+ # <TSeq_sequence>MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
+ #</TSeq>
+
+ def parse( path )
+ Util.check_file_for_readability( path )
+ seqs = Msa.new
+
+ in_seq = false
+ gi = nil
+ accver = nil
+ sid = nil
+ taxid = nil
+ orgname = nil
+ defline = nil
+ seq_str = nil
+ line_counter = 1
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+ File.open( path ) do | file |
+ while line = file.gets
+ line = ic.iconv( line )
+ line_counter += 1
+ if can_ignore?( line )
+
+ elsif line =~ /^\s*<TSeq>/
+ in_seq = true
+
+
+ elsif in_seq
+ if line =~ /^\s*<\/TSeq>/
+ in_seq = false
+ taxonomy = nil
+ if taxid != nil || orgname != nil
+ id_source = nil
+ if taxid != nil
+ id_source = "ncbi"
+ end
+ taxonomy = Taxonomy.new( orgname, taxid , id_source )
+ end
+ id = nil
+ id_source = nil
+ symbol = nil
+ if gi != nil
+ id = gi
+ id_source = "gi"
+ if sid != nil
+ symbol = sid
+ elsif accver != nil
+ symbol = accver
+ end
+ elsif sid != nil
+ id = sid
+ id_source = "ncbi"
+ if accver != nil
+ symbol = accver
+ end
+ elsif accver != nil
+ id = accver
+ id_source = "ncbi"
+ end
+
+ sequence = Sequence.new( defline,
+ seq_str,
+ id,
+ id_source,
+ taxonomy,
+ symbol )
+
+ seqs.add_sequence( sequence )
+ gi = nil
+ accver = nil
+ sid = nil
+ taxid = nil
+ orgname = nil
+ defline = nil
+ seq_str = nil
+ elsif line =~ /^\s*<#{TSEQ_GI}>(\d+)<\/#{TSEQ_GI}>/
+ gi = $1
+ elsif line =~ /^\s*<#{TSEQ_ACCVER}>(.+)<\/#{TSEQ_ACCVER}>/
+ accver = $1
+ elsif line =~ /^\s*<#{TSEQ_SID}>(.+)<\/#{TSEQ_SID}>/
+ sid = $1
+ elsif line =~ /^\s*<#{TSEQ_TAXID}>(\d+)<\/#{TSEQ_TAXID}>/
+ taxid = $1
+ elsif line =~ /^\s*<#{TSEQ_ORGNAME}>(.+)<\/#{TSEQ_ORGNAME}>/
+ orgname = $1
+ elsif line =~ /^\s*<#{TSEQ_DEFLINE}>(.+)<\/#{TSEQ_DEFLINE}>/
+ defline = $1
+ elsif line =~ /^\s*<#{TSEQ_SEQ}>(.+)<\/#{TSEQ_SEQ}>/
+ seq_str = $1
+ elsif line =~ /^\s*<#{TSEQ_TYPE}/
+ elsif line =~ /^\s*<#{TSEQ_LENGTH}/
+ else
+ error_msg = "unexpected line format at line #{line_counter}: " + line
+ raise IOError, error_msg
+ end
+ end
+ end
+ end
+ return seqs
+ end
+
+ private
+
+ def can_ignore?( line )
+ return ( line !~ /\S/ )
+ end
+
+ end # class NcbiTSeqParser
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/io/parser/sp_taxonomy_parser - SpTaxonomyParser class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: sp_taxonomy_parser.rb,v 1.2 2008/12/31 03:21:45 cmzmasek Exp $
+
+
+module Evoruby
+
+ require 'lib/evo/taxonomy/sp_taxonomy'
+
+ class SpTaxonomyParser
+
+ START_OF_COMMENT_LINE_CHAR = "#"
+
+ # raises ArgumentError
+ def SpTaxonomyParser.parse( path )
+ Util.check_file_for_readability( path )
+ row = 0
+ sp_taxonomies = Array.new
+ File.open( path ) do | file |
+ while line = file.gets
+ row += 1
+ if !Util.is_string_empty?( line )
+ if line =~ /([A-Z0-9]{3,5})\s+[A-Z]\s+(\d+):\s+N=(.+)/
+ code = $1
+ id = $2
+ sci_name = $3
+ tax = SpTaxonomy.new(code, id, sci_name )
+ #puts tax.to_str
+ sp_taxonomies.push( tax )
+ end
+ end
+ end
+ end
+ sp_taxonomies
+ end
+ end # class SpTaxonomyParser
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/io/writer/fasta_writer.rb - FastaWriter class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fasta_writer.rb,v 1.6 2008/09/12 23:52:11 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+require 'lib/evo/io/writer/msa_writer'
+
+module Evoruby
+
+ class FastaWriter < MsaWriter
+
+ LINE_WIDTH_DEFAULT = 60
+ MAX_NAME_LENGTH_DEFAULT = 0
+
+ def initialize()
+ @line_width = LINE_WIDTH_DEFAULT
+ @max_name_length = MAX_NAME_LENGTH_DEFAULT
+ @remove_gap_chars = false
+ @clean = false
+ end
+
+
+ def set_line_width( line_width = LINE_WIDTH_DEFAULT )
+ if ( line_width < 1 )
+ line_width = LINE_WIDTH_DEFAULT
+ end
+ @line_width = line_width
+ end
+
+ def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
+ if ( length < 1 )
+ length = MAX_NAME_LENGTH_DEFAULT
+ end
+ @max_name_length = length
+ end
+
+ def remove_gap_chars( remove_gap_chars = true )
+ @remove_gap_chars = remove_gap_chars
+ end
+
+ def clean( clean = true )
+ @clean = clean
+ end
+
+ def write( msa, path )
+ Util.check_file_for_writability( path )
+ f = File.open( path, "a" )
+ for i in 0 ... msa.get_number_of_seqs()
+ seq_obj = msa.get_sequence( i )
+ name = seq_obj.get_name()
+ f.print( ">" )
+ if ( @max_name_length != MAX_NAME_LENGTH_DEFAULT )
+ name = Util.normalize_seq_name( name, @max_name_length )
+ end
+ f.print( name )
+ counter = 0
+ for j in 0 ... seq_obj.get_length()
+ unless @remove_gap_chars && Util.is_aa_gap_character?( seq_obj.get_character_code( j ) )
+ char = seq_obj.get_residue( j )
+ if ( @clean )
+ char = Util.clean_seq_str( char )
+ if ( char.length < 1 )
+ next
+ end
+ end
+ if counter % @line_width == 0
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ end
+ f.print( char )
+ counter += 1
+ end
+ end
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ end
+ f.close()
+ end
+
+ end # class FastaWriter
+
+end # module Evoruby
+
--- /dev/null
+#
+# = lib/evo/io/writer/msa_writer.rb - MsaWriter class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_writer.rb,v 1.2 2007/06/12 04:51:35 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+
+module Evoruby
+
+ class MsaWriter
+
+ def initialize()
+ raise TypeError, "Cannot instanciate abstract class MsaWriter"
+ end
+
+ def set_max_name_length( length )
+ end
+
+ def write( msa, path )
+ end
+
+ end # class MsaWriter
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/writer/nexus_writer.rb - NexusWriter class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: nexus_writer.rb,v 1.4 2009/11/04 01:50:59 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+require 'lib/evo/io/writer/msa_writer'
+
+module Evoruby
+
+ class NexusWriter < MsaWriter
+
+ MAX_NAME_LENGTH_DEFAULT = 10
+
+ def initialize()
+ @max_name_length = MAX_NAME_LENGTH_DEFAULT
+ @clean = false
+ end
+
+ def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
+ if length < 1
+ length = MAX_NAME_LENGTH_DEFAULT
+ end
+ @max_name_length = length
+ end
+
+ def clean( clean = true )
+ @clean = clean
+ end
+
+ def write( msa, path )
+ if ( !msa.is_aligned() )
+ error_msg = "attempt to write unaligned msa in nexus format"
+ raise StandardError, error_msg, caller
+ end
+
+ Util.check_file_for_writability( path )
+
+ f = File.open( path, "a" )
+
+ f.print( "Begin Data;" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ f.print( " Dimensions NTax=" )
+ f.print( msa.get_number_of_seqs().to_s() )
+ f.print( " NChar=" )
+ f.print( msa.get_length().to_s() )
+ f.print( ";" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ f.print( " Format DataType=Protein Interleave=No gap=-;" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ f.print( " Matrix" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ for i in 0 ... msa.get_number_of_seqs()
+ seq_obj = msa.get_sequence( i )
+ name = seq_obj.get_name()
+ seq = seq_obj.get_sequence_as_string()
+ name = name.gsub( /\s+$/, '')
+ name = name.gsub( /\s+/, '_')
+ name = Util.normalize_seq_name( name, @max_name_length )
+ f.print( " " )
+ f.print( name )
+ f.print( " " )
+ if ( @clean )
+ seq = Util.clean_seq_str( seq )
+ end
+ f.print( seq )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ end
+ f.print( " ;" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ f.print( "End;" )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ f.close()
+ end
+
+ end # class NexusWriter
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/io/writer/phylip_sequential_writer.rb - PhylipSequentialWriter class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: phylip_sequential_writer.rb,v 1.4 2008/09/03 00:31:38 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+require 'lib/evo/io/writer/msa_writer'
+
+module Evoruby
+
+ class PhylipSequentialWriter < MsaWriter
+
+ MAX_NAME_LENGTH_DEFAULT = 10
+
+ def initialize()
+ @max_name_length = MAX_NAME_LENGTH_DEFAULT
+ @clean = false
+ end
+
+ def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
+ if length < 1
+ length = MAX_NAME_LENGTH_DEFAULT
+ end
+ @max_name_length = length
+ end
+
+ def clean( clean = true )
+ @clean = clean
+ end
+
+ def write( msa, path )
+ if ( !msa.is_aligned() )
+ error_msg = "attempt to write unaligned msa in phylip sequential format"
+ raise StandardError, error_msg, caller
+ end
+
+
+ Util.check_file_for_writability( path )
+
+ f = File.open( path, "a" )
+
+ f.print( msa.get_number_of_seqs().to_s() )
+ f.print( " " )
+ f.print( msa.get_length().to_s() )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ for i in 0 ... msa.get_number_of_seqs()
+ seq_obj = msa.get_sequence( i )
+ name = seq_obj.get_name()
+ seq = seq_obj.get_sequence_as_string()
+ name = name.gsub( /\s+$/, '')
+ name = name.gsub( /\s+/, '_')
+ name = Util.normalize_seq_name( name, @max_name_length )
+ f.print( name )
+ f.print( " " )
+ if ( @clean )
+ seq = Util.clean_seq_str( seq )
+ end
+ f.print( seq )
+ f.print( Evoruby::Constants::LINE_DELIMITER )
+ end
+ f.close()
+ end
+
+ end # class PhylipSequentialWriter
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/msa/msa.rb - Msa class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa.rb,v 1.11 2009/01/03 00:42:08 cmzmasek Exp $
+#
+
+
+require 'lib/evo/util/constants'
+require 'lib/evo/util/util'
+require 'lib/evo/sequence/sequence'
+
+module Evoruby
+
+ class Msa
+
+ def initialize()
+ @sequences = Array.new()
+ end
+
+
+ def add_sequence( sequence )
+ @sequences.push( sequence )
+ end
+
+ def add( name, molecular_sequence_str )
+ add_sequence( Sequence.new( name, molecular_sequence_str ) )
+ end
+
+ def get_sequence( index )
+ if ( index < 0 || index > get_number_of_seqs() - 1 )
+ error_msg = "attempt to get sequence " <<
+ index.to_s << " in alignment of " << get_number_of_seqs().to_s <<
+ " sequences"
+ raise ArgumentError, error_msg
+ end
+ return @sequences[ index ]
+ end
+
+ def remove_sequence!( index )
+ if ( index < 0 || index > get_number_of_seqs() - 1 )
+ error_msg = "attempt to remove sequence " <<
+ index.to_s << " in alignment of " << get_number_of_seqs().to_s <<
+ " sequences"
+ raise ArgumentError, error_msg
+ end
+ @sequences.delete_at( index )
+ end
+
+ def is_aligned()
+ if ( get_number_of_seqs < 1 )
+ return false
+ else
+ l = @sequences[ 0 ].get_length()
+ for i in 0 ... get_number_of_seqs()
+ if ( get_sequence( i ).get_length() != l )
+ return false
+ end
+ end
+ end
+ return true
+ end
+
+ def find_by_name( name, case_sensitive, partial_match )
+ indices = Array.new()
+ for i in 0 ... get_number_of_seqs()
+ current_name = get_sequence( i ).get_name()
+ if !case_sensitive
+ current_name = current_name.downcase
+ name = name.downcase
+ end
+ if current_name == name ||
+ ( partial_match && current_name.include?( name ) )
+ indices.push( i )
+ end
+ end
+ indices
+ end
+
+ def find_by_name_start( name, case_sensitive )
+ indices = Array.new()
+ for i in 0 ... get_number_of_seqs()
+ get_sequence( i ).get_name() =~ /^\s*(\S+)/
+ current_name = $1
+ if !case_sensitive
+ current_name = current_name.downcase
+ name = name.downcase
+ end
+ if ( current_name == name )
+ indices.push( i )
+ end
+ end
+ indices
+ end
+
+ def has?( name, case_sensitive = true, partial_match = false )
+ for i in 0 ... get_number_of_seqs()
+ current_name = get_sequence( i ).get_name()
+ if !case_sensitive
+ current_name = current_name.downcase
+ name = name.downcase
+ end
+ if current_name == name ||
+ ( partial_match && current_name.include?( name ) )
+ return true
+ end
+ end
+ false
+ end
+
+ # throws ArgumentError
+ def get_by_name( name, case_sensitive = true, partial_match = false )
+ indices = find_by_name( name, case_sensitive, partial_match )
+ if ( indices.length > 1 )
+ error_msg = "\"" + name + "\" not unique"
+ raise ArgumentError, error_msg
+ elsif ( indices.length < 1 )
+ error_msg = "\"" + name + "\" not found"
+ raise ArgumentError, error_msg
+ end
+ get_sequence( indices[ 0 ] )
+ end
+
+ # throws ArgumentError
+ def get_by_name_start( name, case_sensitive = true )
+ indices = find_by_name_start( name, case_sensitive )
+ if ( indices.length > 1 )
+ error_msg = "\"" + name + "\" not unique"
+ raise ArgumentError, error_msg
+ elsif ( indices.length < 1 )
+ error_msg = "\"" + name + "\" not found"
+ raise ArgumentError, error_msg
+ end
+ get_sequence( indices[ 0 ] )
+ end
+
+
+ def get_sub_alignment( seq_numbers )
+ msa = Msa.new()
+ for i in 0 ... seq_numbers.length()
+ msa.add_sequence( get_sequence( seq_numbers[ i ] ).copy() )
+ end
+ return msa
+ end
+
+ def get_number_of_seqs()
+ @sequences.length
+ end
+
+ def get_length()
+ if ( !is_aligned() )
+ error_msg = "attempt to get length of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ if ( get_number_of_seqs() < 1 )
+ -1
+ else
+ @sequences[ 0 ].get_length()
+ end
+ end
+
+ def to_str()
+ s = String.new()
+ for i in 0...get_number_of_seqs()
+ s += @sequences[ i ].to_str + Constants::LINE_DELIMITER
+ end
+ s
+ end
+
+ def print_overlap_diagram( min_overlap = 1, io = STDOUT, max_name_length = 10 )
+ if ( !is_aligned() )
+ error_msg = "attempt to get overlap diagram of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ for i in 0 ... get_number_of_seqs()
+ io.print( Util.normalize_seq_name( get_sequence( i ).get_name(), max_name_length ) )
+ for j in 0 ... get_number_of_seqs()
+ if i == j
+ io.print( " " )
+ else
+ if overlap?( i, j, min_overlap )
+ io.print( "+" )
+ else
+ io.print( "-" )
+ end
+ end
+ end
+ io.print( Evoruby::Constants::LINE_DELIMITER )
+ end
+ end
+
+ #returns array of Msa with an overlap of min_overlap
+ def split_into_overlapping_msa( min_overlap = 1 )
+ if ( !is_aligned() )
+ error_msg = "attempt to split into overlapping msas of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ msas = Array.new()
+ bins = get_overlaps( min_overlap )
+ for i in 0 ... bins.length
+ msas.push( get_sub_alignment( bins[ i ] ) )
+ end
+ msas
+ end
+
+ def overlap?( index_1, index_2, min_overlap = 1 )
+ seq_1 = get_sequence( index_1 )
+ seq_2 = get_sequence( index_2 )
+ overlap_count = 0
+ for i in 0...seq_1.get_length()
+ if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
+ !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
+ overlap_count += 1
+ if overlap_count >= min_overlap
+ return true
+ end
+ end
+ end
+ return false
+ end
+
+ def calculate_overlap( index_1, index_2 )
+ seq_1 = get_sequence( index_1 )
+ seq_2 = get_sequence( index_2 )
+ overlap_count = 0
+ for i in 0...seq_1.get_length()
+ if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
+ !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
+ overlap_count += 1
+ end
+ end
+ overlap_count
+ end
+
+ def calculate_identities( index_1, index_2 )
+ seq_1 = get_sequence( index_1 )
+ seq_2 = get_sequence( index_2 )
+ identities_count = 0
+ for i in 0...seq_1.get_length()
+ if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
+ !Util.is_aa_gap_character?( seq_2.get_character_code( i ) ) &&
+ seq_1.get_character_code( i ) != 63 &&
+ ( seq_1.get_residue( i ).downcase() ==
+ seq_2.get_residue( i ).downcase() )
+ identities_count += 1
+ end
+ end
+ identities_count
+ end
+
+ def remove_gap_only_columns!()
+ remove_columns!( get_gap_only_columns() )
+ end
+
+ def remove_gap_columns!()
+ remove_columns!( get_gap_columns() )
+ end
+
+ # removes columns for which seqs with gap / number of sequences > gap_ratio
+ def remove_gap_columns_w_gap_ratio!( gap_ratio )
+ remove_columns!( get_gap_columns_w_gap_ratio( gap_ratio ) )
+ end
+
+
+ def remove_sequences_by_gap_ratio!( gap_ratio )
+ if ( !is_aligned() )
+ error_msg = "attempt to remove sequences by gap ratio on unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ n = get_number_of_seqs
+ removed = Array.new
+ for s in 0 ... n
+ if ( get_sequence( ( n - 1 ) - s ).get_gap_ratio() > gap_ratio )
+ if ( Evoruby::Constants::VERBOSE )
+ puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
+ end
+ removed << get_sequence( ( n - 1 ) - s ).get_name
+ remove_sequence!( ( n - 1 ) - s )
+ end
+ end
+ removed
+ end
+
+
+ def remove_redundant_sequences!( consider_taxonomy = false, verbose = false )
+ n = get_number_of_seqs
+ removed = Array.new
+ to_be_removed = Set.new
+ for i in 0 ... ( n - 1 )
+ for j in ( i + 1 ) ... n
+ if !to_be_removed.include?( i ) && !to_be_removed.include?( j )
+ if !consider_taxonomy ||
+ ( ( get_sequence( i ).get_taxonomy == nil && get_sequence( j ).get_taxonomy == nil ) ||
+ ( get_sequence( i ).get_taxonomy == get_sequence( j ).get_taxonomy ) )
+ if Util.clean_seq_str( get_sequence( i ).get_sequence_as_string ) ==
+ Util.clean_seq_str( get_sequence( j ).get_sequence_as_string )
+ to_be_removed.add( j )
+ if verbose
+ tax_i = ""
+ tax_j = ""
+ if get_sequence( i ).get_taxonomy != nil
+ tax_i = get_sequence( i ).get_taxonomy.get_name
+ end
+ if get_sequence( j ).get_taxonomy != nil
+ tax_j = get_sequence( j ).get_taxonomy.get_name
+ end
+ puts get_sequence( i ).get_name + " [#{tax_i}] == " + get_sequence( j ).get_name + " [#{tax_j}]"
+ end
+ end
+ end
+ end
+ end
+ end
+ to_be_removed_ary = to_be_removed.to_a.sort.reverse
+
+ to_be_removed_ary.each { | index |
+ removed.push( get_sequence( index ).get_name )
+ remove_sequence!( index )
+ }
+ removed
+ end
+
+
+ def remove_sequences_by_non_gap_length!( min_non_gap_length )
+ if ( !is_aligned() )
+ error_msg = "attempt to remove sequences by non gap length on unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ n = get_number_of_seqs
+ l = get_length
+ removed = Array.new
+ for s in 0 ... n
+ if ( ( l - get_sequence( ( n - 1 ) - s ).get_gap_length ) < min_non_gap_length )
+ if ( Evoruby::Constants::VERBOSE )
+ puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
+ end
+ removed << get_sequence( ( n - 1 ) - s ).get_name
+ remove_sequence!( ( n - 1 ) - s )
+ end
+ end
+ removed
+ end
+
+ def trim!( first, last )
+ cols = Array.new()
+ for i in 0 ... get_length()
+ if ( i < first || i > last )
+ cols.push( i )
+ end
+ end
+ remove_columns!( cols )
+ end
+
+ def get_gap_only_columns()
+ if ( !is_aligned() )
+ error_msg = "attempt to get gap only columns of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ cols = Array.new()
+ for c in 0 ... get_length
+ nogap_char_found = false
+ for s in 0 ... get_number_of_seqs
+ unless Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
+ nogap_char_found = true
+ break
+ end
+ end
+ unless nogap_char_found
+ cols.push( c )
+ end
+ end
+ return cols
+ end
+
+ def get_gap_columns()
+ if ( !is_aligned() )
+ error_msg = "attempt to get gap columns of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ cols = Array.new()
+ for c in 0 ... get_length
+ gap_char_found = false
+ for s in 0 ... get_number_of_seqs
+ if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
+ gap_char_found = true
+ break
+ end
+ end
+ if gap_char_found
+ cols.push( c )
+ end
+ end
+ return cols
+ end
+
+ # gap_ratio = seqs with gap / number of sequences
+ # returns column indices for which seqs with gap / number of sequences > gap_ratio
+ def get_gap_columns_w_gap_ratio( gap_ratio )
+ if ( !is_aligned() )
+ error_msg = "attempt to get gap columns with gap_ratio of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ if ( gap_ratio < 0 || gap_ratio > 1 )
+ error_msg = "gap ratio must be between 0 and 1 inclusive"
+ raise ArgumentError, error_msg, caller
+ end
+ cols = Array.new()
+ for c in 0 ... get_length
+ gap_chars_found = 0
+ for s in 0 ... get_number_of_seqs
+ if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
+ gap_chars_found += 1
+ end
+ end
+ if ( ( gap_chars_found.to_f / get_number_of_seqs ) > gap_ratio )
+ cols.push( c )
+ end
+ end
+ return cols
+ end
+
+
+ # Split an alignment into n alignemnts of equal size, except last one
+ def split( n, verbose = false )
+ if ( n < 2 || n > get_number_of_seqs )
+ error_msg = "attempt to split into less than two or more than the number of sequences"
+ raise StandardError, error_msg, caller
+ end
+ msas = Array.new()
+ r = get_number_of_seqs % n
+ x = get_number_of_seqs / n
+ for i in 0 ... n
+ msa = Msa.new()
+ s = 0
+
+ if ( ( r > 0 ) && ( i == ( n - 1 ) ) )
+ y = x + r
+ if ( verbose )
+ puts( i.to_s + ": " + y.to_s )
+ end
+ for j in 0 ... y
+ msa.add_sequence( get_sequence( ( i * x ) + j ) )
+ end
+ else
+ if ( verbose )
+ puts( i.to_s + ": " + x.to_s )
+ end
+ for j in 0 ... x
+ msa.add_sequence( get_sequence( ( i * x ) + j ) )
+ end
+ end
+ msas.push( msa )
+ end
+ msas
+ end
+
+
+ private
+
+ def get_overlaps( min_overlap = 1 )
+ if ( !is_aligned() )
+ error_msg = "attempt to get overlaps of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ bins = Array.new()
+ for i in 0 ... get_number_of_seqs()
+ found_bin = false
+ for j in 0 ... bins.length
+ current_bin = bins[ j ]
+ # does seq i overlap with all seqs in current_bin?
+ all_overlap = true
+ for z in 0 ... current_bin.length
+ unless overlap?( i, current_bin[ z ], min_overlap )
+ all_overlap = false
+ break
+ end
+ end
+ if all_overlap
+ current_bin.push( i )
+ found_bin = true
+ end
+ end
+ unless found_bin
+ new_bin = Array.new()
+ new_bin.push( i )
+ bins.push( new_bin )
+ end
+ end
+ return bins
+ end
+
+ def remove_columns!( cols )
+ if ( !is_aligned() )
+ error_msg = "attempt to remove columns of unaligned msa"
+ raise StandardError, error_msg, caller
+ end
+ cols.reverse!()
+ for c in 0 ... cols.length()
+ col = cols[ c ]
+ for s in 0 ... get_number_of_seqs()
+ get_sequence( s ).delete_residue!( col )
+ end
+ end
+ return self
+ end
+
+
+ end # class Msa
+
+end # module Evoruby
+
--- /dev/null
+#
+# = lib/evo/msa/msa_factory.rb - MsaFactory class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: msa_factory.rb,v 1.2 2007/06/12 04:51:34 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class MsaFactory
+
+ def initialize
+ end
+
+ def create_msa_from_file( path, msa_parser )
+ msa_parser.parse( path )
+ end
+
+ end # class MsaFactory
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/sequence/domain_structure.rb - DomainStructure class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: domain_structure.rb,v 1.2 2007/06/12 04:51:33 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+require 'lib/evo/util/constants'
+
+module Evoruby
+
+ class DomainStructure
+
+ def initialize( total_length )
+ @domains = Hash.new
+ @total_length = total_length
+ end
+
+ def add_domain( domain, overwrite_if_same_from_to )
+ key = domain.get_from
+ if ( @domains.has_key?( key ) )
+ prev_domain = @domains[ key ]
+ if ( prev_domain.get_to == domain.get_to )
+ puts( "WARNING: more than one domain at the same location [" +
+ key.to_s + "-" + domain.get_to.to_s + "]: " + prev_domain.get_name + " and " + domain.get_name)
+ if ( overwrite_if_same_from_to )
+ puts( " ignored the one with higher E-value [" +
+ prev_domain.get_confidence().to_s + " vs " + domain.get_confidence().to_s + "]" )
+ if prev_domain.get_confidence() < domain.get_confidence()
+ return # keep previous one
+ else
+ @domains[ key ] = domain
+ return
+ end
+ end
+ end
+
+ while ( @domains.has_key?( key ) )
+ key = key + 0.0001
+ end
+
+ end
+ @domains[ key ] = domain
+ end
+
+ def to_NHX
+ str = String.new
+ str << get_total_length.to_s
+ a = @domains.sort
+ for d in a
+ domain = d[ 1 ]
+ str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
+ str << domain.get_from.to_s
+ str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
+ str << domain.get_to.to_s
+ str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
+ str << domain.get_confidence.to_s
+ str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
+ str << domain.get_name
+ end
+ return str
+ end
+
+ def get_total_length
+ return @total_length
+ end
+
+ end # class DomainStructure
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/sequence/protein_domain.rb - ProteinDomain class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: protein_domain.rb,v 1.2 2007/06/12 04:51:33 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class ProteinDomain
+
+ def initialize( name, from, to, id, confidence )
+ @name = String.new( name )
+ @from = from
+ @to = to
+ @id = String.new( id )
+ @confidence = confidence
+ end
+
+ def get_name()
+ return @name
+ end
+
+ def get_from()
+ return @from
+ end
+
+ def get_to()
+ return @to
+ end
+
+ def get_id()
+ return @id
+ end
+
+ def get_confidence()
+ return @confidence
+ end
+
+ end # class ProteinDomain
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/sequence/sequence.rb - Sequence class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: sequence.rb,v 1.10 2009/01/07 02:48:20 cmzmasek Exp $
+
+require 'set'
+
+module Evoruby
+
+ class Sequence
+
+ def initialize( name,
+ molecular_sequence_str,
+ accession = nil,
+ accession_source = nil,
+ taxonomy = nil,
+ symbol = nil,
+ secondary_accession = nil,
+ secondary_accession_source = nil )
+ @name = String.new( name.strip() )
+ @molecular_sequence = String.new( molecular_sequence_str )
+ if ( accession == nil )
+ @accession = String.new()
+ else
+ @accession = String.new( accession.strip() )
+ end
+ if ( accession_source == nil )
+ @accession_source = String.new()
+ else
+ @accession_source = String.new( accession_source.strip() )
+ end
+ @taxonomy = taxonomy
+ if ( symbol == nil )
+ @symbol = String.new()
+ else
+ @symbol = String.new( symbol.strip() )
+ end
+ if ( secondary_accession == nil )
+ @secondary_accession = String.new()
+ else
+ @secondary_accession = String.new( secondary_accession.strip() )
+ end
+ if ( secondary_accession_source == nil )
+ @secondary_accession_source = String.new()
+ else
+ @secondary_accession_source = String.new( secondary_accession_source.strip() )
+ end
+ end
+
+ def copy
+ if get_taxonomy == nil
+ Sequence.new( get_name, get_sequence_as_string, get_accession, get_accession_source, nil, get_symbol, get_secondary_accession, get_secondary_accession_source )
+ else
+ Sequence.new( get_name, get_sequence_as_string, get_accession, get_accession_source, get_taxonomy.copy, get_symbol, get_secondary_accession, get_secondary_accession_source )
+ end
+ end
+
+ def get_name()
+ @name
+ end
+
+ def set_name( name )
+ @name = name
+ end
+
+ def get_sequence_as_string()
+ @molecular_sequence
+ end
+
+ def get_accession()
+ @accession
+ end
+
+ def get_accession_source()
+ @accession_source
+ end
+
+ def get_secondary_accession()
+ @secondary_accession
+ end
+
+ def get_secondary_accession_source()
+ @secondary_accession_source
+ end
+
+ def get_symbol()
+ @symbol
+ end
+
+ def get_taxonomy()
+ @taxonomy
+ end
+
+ def get_length()
+ @molecular_sequence.length
+ end
+
+ def get_residue( position )
+ get_slice( position, 1 )
+ end
+
+ def get_character_code( position )
+ @molecular_sequence.getbyte( position )
+ end
+
+ def get_gap_ratio()
+ return get_gap_length().to_f / get_length()
+ end
+
+ def get_gap_length()
+ counter = 0
+ for i in 0 ... get_length()
+ if ( Util.is_aa_gap_character?( get_character_code( i ) ) )
+ counter += 1
+ end
+ end
+ return counter;
+ end
+
+ def delete_residue!( position )
+ if ( position < 0 || position >= get_length() )
+ error_msg = "attempt to delete residue at postion out of range"
+ raise ArgumentError, error_msg
+ end
+ @molecular_sequence.slice!( position )
+ end
+
+ def get_slice( start, length )
+ if ( start < 0 || start + length > get_length() )
+ error_msg = "attempt to get sequence residue(s) at postion out of range"
+ raise ArgumentError, error_msg
+ end
+ @molecular_sequence.slice( start, length )
+ end
+
+ def get_slice!( start, length )
+ if ( start < 0 || start + length > get_length() )
+ error_msg = "attempt to get sequence residue(s) at postion out of range"
+ raise ArgumentError, error_msg
+ end
+ @molecular_sequence.slice!( start, length )
+ end
+
+ def get_subsequence( first, last )
+ if ( last < first )
+ error_msg = "attempt to get subsequence from " + first + " to " + last
+ raise ArgumentError, error_msg
+ end
+ return Sequence.new( get_name, @molecular_sequence.slice( first, last - first + 1 ) )
+ end
+
+ def append!( molecular_sequence_str )
+ @molecular_sequence.concat( molecular_sequence_str )
+ end
+
+ def to_str()
+ return "[" + @name + "] " + @molecular_sequence
+ end
+
+ end # class Sequence
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/soft/fastme - FastMe class
+#
+# Copyright:: Copyright (C) 2009 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: fastme.rb,v 1.3 2009/10/08 22:44:54 cmzmasek Exp $
+#
+# last modified: 2009/10/06
+
+require 'lib/evo/soft/resource_locations'
+require 'lib/evo/util/util'
+
+module Evoruby
+
+ class FastMe
+
+ VERBOSE = false
+
+ OUTTREE = 'output.tre'
+ OUTPUT_D = 'output.d'
+ VERSION = '2.0'
+
+ def initialize
+ @fast_me_home = Util.get_env_variable_value( ResourceLocations::FASTME_HOME_ENV_VARIABLE )
+ Util.check_file_for_readability( @fast_me_home )
+ end
+
+ def run( pwd_file, bootstrap_number, initial_tree )
+ Util.check_file_for_readability( pwd_file )
+ if bootstrap_number == nil || bootstrap_number < 0
+ error_msg = "illegal bootstrap number: " + bootstrap_number
+ raise ArgumentError, error_msg
+ end
+ init_tree_option = determine_initial_tree( initial_tree )
+ input = String.new()
+ if bootstrap_number > 1
+ input = "-b #{init_tree_option} -i #{pwd_file} -n #{bootstrap_number} -s b"
+ else
+ input = "-b #{init_tree_option} -i #{pwd_file} -s b"
+ end
+ if VERBOSE
+ puts @fast_me_home + " " + input
+ end
+ IO.popen( @fast_me_home + " " + input, 'r+' ) do |io|
+ io.close_write
+ return io.read
+ end
+ end
+
+ private
+
+ def determine_initial_tree( initial_tree )
+ opt = nil
+ if ( initial_tree == :BME )
+ opt = "BME"
+ elsif ( initial_tree == :GME )
+ opt = "GME"
+ elsif ( initial_tree == :NJ )
+ opt = "NJ"
+ else
+ error_msg = "unknown initial tree"
+ raise ArgumentError, error_msg
+ end
+ return opt
+ end
+
+ end # class FastMe
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/soft/raxml - Raxml class
+#
+# Copyright:: Copyright (C) 2009 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: raxml.rb,v 1.1 2009/10/07 00:08:35 cmzmasek Exp $
+#
+# last modified: 2009/10/06
+
+require 'lib/evo/soft/resource_locations'
+require 'lib/evo/util/util'
+
+module Evoruby
+
+ class Raxml
+
+ VERBOSE = true
+
+ def initialize
+ @fast_me_home = Util.get_env_variable_value( ResourceLocations::FASTME_HOME_ENV_VARIABLE )
+ Util.check_file_for_readability( @fast_me_home )
+ end
+
+ def run( pwd_file, bootstrap_number, initial_tree )
+ Util.check_file_for_readability( pwd_file )
+ if bootstrap_number == nil || bootstrap_number < 0
+ error_msg = "illegal bootstrap number: " + bootstrap_number
+ raise ArgumentError, error_msg
+ end
+ if initial_tree == nil || (!initial_tree.eql?( "BME" ) && !initial_tree.eql?( "GME" ) && !initial_tree.eql?( "NJ" ) )
+ error_msg = "illegal initial tree: " + initial_tree
+ raise ArgumentError, error_msg
+ end
+ input = String.new()
+ if bootstrap_number > 1
+ input = '-b #{initial_tree} -i #{pwd_file} -n #{bootstrap_number} -s b'
+ else
+ input = '-b #{initial_tree} -i #{pwd_file} -s b'
+ end
+ if VERBOSE
+ puts @fast_me_home + " " + input
+ end
+ IO.popen( @fast_me_home, 'r+' ) do |io|
+ io.puts input
+ io.close_write
+ return io.read
+ end
+ end
+ end # class Raxml
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/soft/resource_locations - ResourceLocations class
+#
+# Copyright:: Copyright (C) 2009 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: resource_locations.rb,v 1.1 2009/10/06 22:22:46 cmzmasek Exp $
+#
+# last modified: 2009/10/06
+
+
+module Evoruby
+
+ class ResourceLocations
+
+ FASTME_HOME_ENV_VARIABLE = 'FASTME_HOME'
+ TREEPUZZLE_HOME_ENV_VARIABLE = 'TREEPUZZLE_HOME'
+
+ end # ResourceLocations
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/soft/tree_puzzle - TreePuzzle class
+#
+# Copyright:: Copyright (C) 2009 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: tree_puzzle.rb,v 1.5 2009/10/08 22:44:54 cmzmasek Exp $
+#
+# last modified: 2009/10/06
+
+require 'lib/evo/soft/resource_locations'
+require 'lib/evo/util/util'
+
+module Evoruby
+
+ class TreePuzzle
+
+ VERBOSE = false
+
+ OUTDIST = 'outdist'
+ OUTFILE = 'outfile'
+ VERSION = '5.2'
+
+ def initialize
+ @tree_puzzle_home = Util.get_env_variable_value( ResourceLocations::TREEPUZZLE_HOME_ENV_VARIABLE )
+ Util.check_file_for_readability( @tree_puzzle_home )
+ end
+
+ def run( alignment_file, model, rate_heterogeneity, number_of_seqs )
+ Util.check_file_for_readability( alignment_file )
+
+ input = alignment_file
+ input << "\nk\nk"
+ if number_of_seqs <= 257
+ input << "\nk"
+ end
+ input << determine_model_option( model )
+ input << determine_rate_heterogeneity_option( rate_heterogeneity )
+ input << "\ny\n"
+
+ if VERBOSE
+ puts @tree_puzzle_home + " " + input
+ end
+ IO.popen( @tree_puzzle_home, 'r+' ) do |io|
+ io.puts input
+ io.close_write
+ return io.read
+ end
+ end
+
+ private
+
+ # "Model of substitution" order for DQO TREE-PUZZLE 5.0:
+ # Auto
+ # m -> Dayhoff (Dayhoff et al. 1978)
+ # m -> JTT (Jones et al. 1992)
+ # m -> mtREV24 (Adachi-Hasegawa 1996)
+ # m -> BLOSUM62 (Henikoff-Henikoff 92)
+ # m -> VT (Mueller-Vingron 2000)
+ # m -> WAG (Whelan-Goldman 2000)
+ # m -> Auto
+ def determine_model_option( model )
+ cmd = nil
+ if ( model == :pam )
+ cmd = "\nm"
+ elsif ( model == :jtt )
+ cmd = "\nm\nm"
+ elsif ( model == :mtrev24 )
+ cmd = "\nm\nm\nm"
+ elsif ( model == :blosum62 )
+ cmd = "\nm\nm\nm\nm"
+ elsif ( model == :vt )
+ cmd = "\nm\nm\nm\nm\nm"
+ elsif ( model == :wag )
+ cmd = "\nm\nm\nm\nm\nm\nm"
+ elsif ( model == :auto )
+ cmd = ""
+ else
+ error_msg = "unknown model"
+ raise ArgumentError, error_msg
+ end
+ cmd
+ end
+
+
+ # Model of rate heterogeneity:
+ # "8 Gamma distributed rates"
+ # "Two rates (1 invariable + 1 variable)"
+ # "Mixed (1 invariable + 8 Gamma rates)"
+ # otherwise: Uniform rate
+ def determine_rate_heterogeneity_option( rates )
+ opt = nil
+ if ( rates == :gamma8 )
+ opt = "\nw"
+ elsif ( rates == :inv1_var1 )
+ opt = "\nw\nw"
+ elsif ( rates == :inv1_gamma8 )
+ opt = "\nw\nw\nw"
+ elsif ( rates == :uniform )
+ opt = ""
+ else
+ error_msg = "unknown rate heterogeneity option"
+ raise ArgumentError, error_msg
+ end
+ return opt
+ end
+
+ end # class TreePuzzle
+
+end # module Evoruby
--- /dev/null
+# = lib/evo/table/basic_table.rb - BasicTable class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)'s
+#
+# $Id: basic_table.rb,v 1.3 2007/09/28 03:12:10 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+#require 'lib/evo/util/constants'
+
+module Evoruby
+
+ class BasicTable
+
+ def initialize()
+ @rows = Hash.new
+ @max_row = 0
+ @max_col = 0
+ end
+
+ # raises ArgumentError
+ def set_value( row, col, value )
+ if ( ( row < 0 ) || ( col < 0 ) )
+ raise( ArgumentError, "attempt to use negative values for row or column" )
+ end
+ if ( row > get_max_row() )
+ set_max_row( row )
+ end
+ if ( col > get_max_col() )
+ set_max_col( col )
+ end
+ row_map = nil
+ if ( @rows.has_key?( row ) )
+ row_map = @rows[ row ]
+ else
+ row_map = Hash.new
+ @rows[ row ] = row_map
+ end
+ row_map[ col ] = value
+ end
+
+ # raises ArgumentError
+ def get_value_as_string( row, col )
+ return ( get_value( row, col ) ).to_s
+ end
+
+ # raises ArgumentError
+ def get_value( row, col )
+ if ( ( row > get_max_row() ) || ( row < 0 ) )
+ raise( ArgumentError, "value for row (" + row.to_s +
+ ") is out of range [max row: " + get_max_row().to_s + "]" )
+ elsif ( ( col > get_max_col() ) || ( row < 0 ) )
+ raise( ArgumentError, "value for column (" + col.to_s +
+ ") is out of range [max column: " + get_max_col().to_s + "]" )
+ end
+ row_map = @rows[ row ]
+ if ( ( row_map == nil ) || ( row_map.length < 1 ) )
+ return nil
+ end
+ return row_map[ col ]
+ end
+
+ def get_max_col()
+ return @max_col
+ end
+
+ def get_max_row()
+ return @max_row
+ end
+
+ # raises ArgumentError
+ def get_columns_as_map( key_col, value_col )
+ map = Hash.new
+ for row in 0 .. get_max_row
+ key = get_value( row, key_col )
+ value = get_value( row, value_col )
+ if ( ( key != nil ) && ( value != nil ) )
+ if ( map.has_key?( key ) )
+ raise( ArgumentError, "attempt to use non-unique table value as key [" +
+ + key + "]" )
+ end
+ map[ key ] = value
+ end
+ end
+ return map
+ end
+
+ def to_s
+ str = String.new
+ for row in 0 .. get_max_row
+ for col in 0 .. get_max_col
+ str << col.to_s << " "
+ end
+ str << LEvoruby::Constants::LINE_DELIMITER
+ for col in 0 .. get_max_col
+ str << row.to_s << ": "
+ str << get_value( row, col ) << " "
+ end
+ str << Evoruby::Constants::LINE_DELIMITER
+ end
+ return str
+ end
+
+
+ private
+
+ def get_row( row )
+ return @rows[ row ]
+ end
+
+ def set_max_col( max_col )
+ @max_col = max_col
+ end
+
+ def set_max_row( max_row )
+ @max_row = max_row
+ end
+
+ end # class BasicTable
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/taxonomy/sp_taxonomy.rb - SpTaxonomy class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: sp_taxonomy.rb,v 1.1 2008/12/30 05:28:00 cmzmasek Exp $
+
+
+
+module Evoruby
+
+ class SpTaxonomy
+
+ attr_accessor :code, :id, :scientific_name, :common_name
+
+ def initialize( code, id, scientific_name, common_name = nil )
+ @code = String.new( code.strip() )
+ @id = String.new( id.strip() )
+ @scientific_name = String.new( scientific_name.strip() )
+ if ( common_name == nil )
+ @common_name = String.new()
+ else
+ @common_name = String.new( common_name.strip() )
+ end
+ end
+
+ def copy
+ return Taxonomy.new( code, id, scientific_name, common_name )
+ end
+
+ def to_str()
+ code + " " + id + ": N=" + scientific_name
+ end
+
+ end # class SpTaxonomy
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/taxonomy/taxonomy.rb - Taxonomy class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: taxonomy.rb,v 1.2 2009/01/03 00:19:08 cmzmasek Exp $
+
+
+
+module Evoruby
+
+ class Taxonomy
+
+ def initialize( name, id = nil, id_source = nil )
+ @name = String.new( name.strip() )
+ if ( id == nil )
+ @id = String.new()
+ else
+ @id = String.new( id.strip() )
+ end
+ if ( id_source == nil )
+ @id_source = String.new()
+ else
+ @id_source = String.new( id_source.strip() )
+ end
+ end
+
+ def == ( taxonomy )
+ if taxonomy == nil
+ return false
+ else
+ return ( ( get_name == taxonomy.get_name ) &&
+ ( get_id == taxonomy.get_id ) &&
+ ( get_id_source == taxonomy.get_id_source ) )
+ end
+ end
+
+ def copy
+ return Taxonomy.new( get_name, get_id, get_id_source )
+ end
+
+ def get_name()
+ @name
+ end
+
+ def get_id()
+ @id
+ end
+
+ def get_id_source()
+ @id_source
+ end
+
+ def to_str()
+ if Util.is_string_empty?( get_id )
+ @name
+ else
+ "[" + get_id + "] " + @name
+ end
+ end
+
+ end # class Taxonomy
+
+end # module Evoruby
\ No newline at end of file
--- /dev/null
+#
+# = lib/evo/util/command_line_arguments.rb - CommandLineArguments class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: command_line_arguments.rb,v 1.2 2007/06/12 04:51:34 cmzmasek Exp $
+#
+# last modified: 05/16/2007
+
+module Evoruby
+
+ class CommandLineArguments
+
+ OPTIONS_PREFIX = "-"
+ EXTENDED_OPTIONS_PREFIX = "--"
+ OPTIONS_SEPARATOR = "="
+
+ # raises ArgumentError
+ def initialize( args )
+ @options = Hash.new
+ @extended_options = Hash.new
+ @file_names = Array.new
+ parse_arguments( args )
+ end
+
+ def get_file_names
+ return @file_names
+ end
+
+ def get_file_name( i )
+ return @file_names[ i ]
+ end
+
+ def get_number_of_files()
+ return @file_names.length
+ end
+
+ def is_option_set?( option_name )
+ o = get_all_options
+ return ( o.has_key?( option_name ) )
+ end
+
+ # raises ArgumentError
+ def get_option_value( option_name )
+ o = get_all_options
+ if ( o.has_key?( option_name ) )
+ value = o[ option_name ]
+ if ( !Util.is_string_empty?( value ) )
+ return value
+ else
+ raise( ArgumentError, "value for option \"" +
+ option_name + "\" is not set", caller )
+ end
+ else
+ raise( ArgumentError, "option \"" + option_name +
+ "\" is not set", caller )
+ end
+ end
+
+ def get_option_value_as_int( option_name )
+ return get_option_value( option_name ).to_i
+ end
+
+ def get_option_value_as_float( option_name )
+ return get_option_value( option_name ).to_f
+ end
+
+ # mandatory_options (Array)
+ #
+ def validate_mandatory_options( mandatory_options )
+ o = get_all_options
+ missing = Array.new
+ for ma in mandatory_options
+ if ( !o.has_key?( ma ) )
+ missing.push( ma )
+ end
+ end
+ return missing
+ end
+
+ # mandatory_options (Array)
+ #
+ def validate_mandatory_options_as_str( mandatory_options )
+ missing = validate_mandatory_options( mandatory_options )
+ return missing.join( ", " )
+ end
+
+ # allowed_options (Array)
+ #
+ def validate_allowed_options( allowed_options )
+ o = get_all_options
+ disallowed = Array.new
+ o.each_key { |op|
+ if ( !allowed_options.include?( op ) )
+ disallowed.push( op )
+ end
+ }
+ return disallowed
+ end
+
+ # allowed_options (Array)
+ #
+ def validate_allowed_options_as_str( allowed_options )
+ disallowed = validate_allowed_options( allowed_options )
+ return disallowed.join( ", " )
+ end
+
+ private
+
+ def get_all_options
+ o = Hash.new
+ o.merge!( get_options_list )
+ o.merge!( get_extended_options_list )
+ return o
+ end
+
+ def parse_arguments( args )
+ for arg in args
+ if ( arg.index( EXTENDED_OPTIONS_PREFIX ) == 0 )
+ parse_option( arg.slice( EXTENDED_OPTIONS_PREFIX.length, arg.length() - 1 ),
+ get_extended_options_list )
+
+ elsif ( arg.index( OPTIONS_PREFIX ) == 0 )
+ parse_option( arg.slice( OPTIONS_PREFIX.length, arg.length() - 1 ),
+ get_options_list )
+
+ else
+ get_file_names.push( arg )
+ end
+ end
+ end
+
+ # raises ArgumentError
+ def parse_option( option, options_map )
+ sep_index = option.index( OPTIONS_SEPARATOR )
+ if ( sep_index == nil )
+ if ( Util.is_string_empty?( option ) )
+ raise( ArgumentError, "attempt to set option with an empty name" )
+ end
+ if ( get_all_options.has_key?( option ) )
+ raise( ArgumentError, "attempt to set option \"" +
+ option + "\" mutiple times" )
+ end
+ options_map[ option ] = ""
+ else
+ key = option.slice( 0, sep_index )
+ value = option.slice( sep_index + 1, option.length() - 1 )
+ if ( Util.is_string_empty?( key ) )
+ raise( ArgumentError, "attempt to set option with an empty name" )
+ end
+ if ( Util.is_string_empty?( value ) )
+ raise( ArgumentError, "attempt to set option with an empty value" )
+ end
+ if ( get_all_options.has_key?( key ) )
+ raise( ArgumentError, "attempt to set option \"" +
+ key + "\" mutiple times [" + option + "]" )
+ end
+ options_map[ key ] = value
+ end
+ end
+
+ def get_file_names_list
+ return @file_names
+ end
+
+ def get_options_list
+ return @options
+ end
+
+ def get_extended_options_list
+ return @extended_options
+ end
+
+ end # class CommandLineArguments
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/util/constants.rb - Constants class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: constants.rb,v 1.3 2007/12/21 04:13:33 cmzmasek Exp $
+#
+# last modified: 05/11/2007
+
+module Evoruby
+
+ class Constants
+
+ VERBOSE = true
+
+ EVORUBY_VERSION = '1.0'
+
+ FORESTER_HOME_ENV_VARIABLE = 'FORESTER_HOME'
+ JAVA_HOME_ENV_VARIABLE = 'JAVA_HOME'
+
+ EVORUBY = 'evoruby'
+
+ LINE_DELIMITER = "\n"
+
+ FILE_SEPARATOR = File::SEPARATOR
+
+ DOMAIN_STRUCTURE_NHX_SEPARATOR = '>'
+
+
+ end # class Constants
+
+end # module Evoruby
--- /dev/null
+#
+# = lib/evo/util/util.rb - Util class
+#
+# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: util.rb,v 1.17 2009/10/06 22:22:46 cmzmasek Exp $
+#
+# last modified: 05/15/2007
+
+require 'lib/evo/util/constants'
+
+module Evoruby
+
+ class Util
+
+ def Util.normalize_seq_name( name, length )
+ if name.length > length
+ name = name[ 0, length ]
+ elsif name.length < length
+ for i in 0 ... length - name.length
+ name = name + " "
+ end
+ end
+ name
+ end
+
+ # def Util.normalize_mol_sequence( seq )
+ # new_seq = String.new()
+ # for i in 0 ... seq.length
+ # c = seq.get_slice( i )
+ # if is_aa_gap_character?( c )
+ # new_seq = new_seq + "-"
+ # else
+ # new_seq = new_seq + c
+ # end
+ # end
+ # new_seq
+ # end
+
+
+ # Returns true if char_code corresponds to: space * - . _
+ def Util.is_aa_gap_character?( char_code )
+ return ( char_code <= 32 || char_code == 42 || char_code == 45 || char_code == 46 ||char_code == 95 )
+ end
+
+ # Deletes *, digits, and whitespace, replaces BJOUZ? with X, and replaces non-(letters, -) with -
+ def Util.clean_seq_str( seq_str )
+ seq_str = seq_str.upcase
+ seq_str = seq_str.gsub( /\s+/, '' )
+ seq_str = seq_str.gsub( /\d+/, '' )
+ seq_str = seq_str.gsub( '*', '' )
+ seq_str = seq_str.gsub( /[BJOUZ?]/, 'X' )
+ seq_str = seq_str.gsub( /[^A-Z\-]/, '-' )
+ seq_str
+ end
+
+ # raises ArgumentError
+ def Util.check_file_for_readability( path )
+ unless ( File.exist?( path ) )
+ error_msg = "file [#{path}] does not exist"
+ raise ArgumentError, error_msg
+ end
+ unless ( File.file?( path ) )
+ error_msg = "file [#{path}] is not a regular file"
+ raise ArgumentError, error_msg
+ end
+ unless ( File.readable?( path ) )
+ error_msg = "file [#{path}] is not a readable file"
+ raise ArgumentError, error_msg
+ end
+ if ( File.zero?( path ) )
+ error_msg = "file [#{path}] is empty"
+ raise ArgumentError, error_msg
+ end
+ end
+
+ # raises ArgumentError
+ def Util.check_file_for_writability( path )
+ if File.directory?( path )
+ error_msg = "file [#{path}] is an existing directory"
+ raise ArgumentError, error_msg
+ elsif File.exist?( path )
+ error_msg = "file [#{path}] already exists"
+ raise ArgumentError, error_msg
+ elsif File.writable?( path )
+ error_msg = "file [#{path}] is not writeable"
+ raise ArgumentError, error_msg
+ end
+ end
+
+ def Util.fatal_error_if_not_writable( prg_name, path )
+ begin
+ Util.check_file_for_writability( path )
+ rescue ArgumentError => e
+ Util.fatal_error( prg_name, e.to_s )
+ end
+ end
+
+ def Util.fatal_error_if_not_readable( prg_name, path )
+ begin
+ Util.check_file_for_readability( path )
+ rescue ArgumentError => e
+ Util.fatal_error( prg_name, e.to_s )
+ end
+ end
+
+ def Util.get_env_variable_value( env_variable )
+ value = ENV[env_variable]
+ if value == nil || value.empty?
+ error_msg = "apparently environment variable #{env_variable} has not been set"
+ raise StandardError, error_msg
+ end
+ value
+ end
+
+
+ # raises ArgumentError
+ def Util.file2array( path, split_by_semicolon )
+ Util.check_file_for_readability( path )
+ a = Array.new()
+ c = 0
+ File.open( path ) do | file |
+ while line = file.gets
+ if ( line =~ /^\s*(\S.*?)\s*$/ )
+ s = $1
+ if ( split_by_semicolon && s =~/;/ )
+ sa = s.split( /;/ )
+ for i in 0 ... sa.length()
+ a[ c ] = sa[ i ].strip!
+ end
+ else
+ a[ c ] = s
+ end
+ c += 1
+ end
+ end
+ end
+ return a
+ end
+
+ def Util.print_program_information( prg_name,
+ prg_version,
+ prg_desc,
+ date,
+ copyright,
+ contact,
+ www,
+ io = STDOUT )
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ ruby_version = RUBY_VERSION
+ l = prg_name.length + prg_version.length + date.length + ruby_version.length + 12
+ io.print( Evoruby::Constants::LINE_DELIMITER )
+ io.print( prg_name + " " + prg_version + " [" + date + "] [ruby " + ruby_version + "]")
+ io.print( Evoruby::Constants::LINE_DELIMITER )
+ l.times {
+ io.print( "_" )
+ }
+ io.print( Constants::LINE_DELIMITER )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( prg_desc )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( "Copyright (C) " + copyright )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( "Contact: " + contact )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( " " + www )
+ io.print( Constants::LINE_DELIMITER )
+ io.print( Constants::LINE_DELIMITER )
+ end
+
+ def Util.fatal_error( prg_name, message, io = STDOUT )
+ io.print( Constants::LINE_DELIMITER )
+ if ( !Util.is_string_empty?( prg_name ) )
+ io.print( "[" + prg_name + "] > " + message )
+ else
+ io.print( " > " + message )
+ end
+ io.print( Constants::LINE_DELIMITER )
+ io.print( Constants::LINE_DELIMITER )
+ exit( -1 )
+ end
+
+ def Util.print_message( prg_name, message, io = STDOUT )
+ if ( !Util.is_string_empty?( prg_name ) )
+ io.print( "[" + prg_name + "] > " + message )
+ else
+ io.print( " > " + message )
+ end
+ io.print( Constants::LINE_DELIMITER )
+ end
+
+ def Util.print_warning_message( prg_name, message, io = STDOUT )
+ if ( !Util.is_string_empty?( prg_name ) )
+ io.print( "[" + prg_name + "] > WARNING: " + message )
+ else
+ io.print( " > " + message )
+ end
+ io.print( Constants::LINE_DELIMITER )
+ end
+
+ def Util.is_string_empty?( s )
+ return ( s == nil || s.length < 1 )
+ end
+
+ # From "Ruby Cookbook"
+ # counts_hash: key is a "name", value is the count (integer)
+ def Util.draw_histogram( counts_hash, char = "#" )
+ pairs = counts_hash.keys.collect { |x| [ x.to_s, counts_hash[ x ] ] }.sort
+ largest_key_size = pairs.max { |x, y| x[ 0 ].size <=> y[ 0 ].size }[ 0 ].size
+ pairs.inject( "" ) do | s, kv |
+ s << "#{ kv[ 0 ].ljust( largest_key_size ) } | #{ char*kv[ 1 ] }" + Constants::LINE_DELIMITER
+ end
+ end
+
+ def Util.looks_like_fasta?( path )
+ Util.check_file_for_readability( path )
+ File.open( path ) do | file |
+ while line = file.gets
+ if ( line !~ /\S/ || line =~ /^\s*#/ )
+ elsif line =~ /^\s*>\s*(.+)/
+ return true
+ else
+ return false
+ end
+ end
+ end
+ error_msg = "unexpected format"
+ raise IOError, error_msg
+ end
+
+ end # class Util
+
+end # module Evoruby
--- /dev/null
+#!/usr/local/bin/ruby -w
+
+infile = ARGV[ 0 ]
+
+metazoa_choanoflagellata = [
+"Metazoa_Choanoflagellata",
+"Metazoa",
+"Bilateria_Cnidaria",
+"Bilateria",
+"Deuterostomia",
+"Chordata",
+"Urochordata_Vertebrata",
+"Vertebrata",
+"Tetrapoda",
+"Amniota",
+"Eutheria",
+"Euarchontoglires",
+"Primates",
+"Rodentia",
+"Teleostei",
+"Euteleostei",
+"Smegmamorpha",
+"Tetraodontiformes",
+"Urochordata",
+"Ascidiacea",
+"Urochordata",
+"Protostomia",
+"Ecdysozoa",
+"Arthropoda",
+"Insecta",
+"Lepidoptera_Diptera_Hymenoptera",
+"Diptera",
+"Culicoidea",
+"Hymenoptera",
+"Nematoda",
+"Annelida_Mollusca",
+"Annelida" ]
+
+if infile == nil
+ puts "no infile"
+ exit
+end
+
+File.open( infile ) do | file |
+ while line = file.gets
+ if line =~ /^[0-9A-Z]{3,5}\s/
+ elsif line =~ /^\t/
+ elsif line =~ /^{/
+ elsif line =~ /^f_\d/
+ else
+ line =~ /(\S+)/
+ first = $1
+ if metazoa_choanoflagellata.include?( first )
+ puts( line )
+ end
+ end
+ end
+end
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = hmm_split
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: hmm_split.rb,v 1.5 2008/11/17 22:32:43 cmzmasek Exp $
+#
+# To split a Pfam HMM file into one file for each HMM.
+#
+
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+
+ if ( ARGV == nil || ARGV.length != 3 )
+ puts( "usage: hmm_split.rb <Pfam HMM file> <outfile suffix> <outdir>" )
+ exit( -1 )
+ end
+
+ hmmfile = ARGV[ 0 ]
+ suffix = ARGV[ 1 ]
+ outdir = ARGV[ 2 ]
+
+ if ( !File.exists?( outdir ) )
+ puts( "outdir [" + outdir + "] does not exist" )
+ exit( -1 )
+ end
+ if ( !File.exists?( hmmfile ) )
+ puts( "Pfam HMM file [" + hmmfile + "] does not exist" )
+ exit( -1 )
+ end
+
+ data = String.new
+ name = String.new
+ line_count = 0
+ count = 0
+
+ File.open( hmmfile ) do | file |
+ while line = file.gets
+ data = data + line
+ line_count += 1
+ if ( line =~ /NAME\s+(.+)/ )
+ if name.length > 0
+ puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ name = $1
+ elsif ( line =~ /\/\// )
+ if name.length < 1
+ puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+
+ outfile = outdir + '/' + name + suffix
+ if ( File.exists?( outfile ) )
+ puts( "file [" + outfile + "] already exists" )
+ exit( -1 )
+ end
+ open( outfile, 'w' ) do | out |
+ out.write( data )
+ end
+ count += 1
+ puts( count.to_s + ": " + name )
+ data = String.new
+ name = String.new
+ end
+ end
+ end
+
+ puts()
+ puts( "wrote " + count.to_s + " individual HMM files to " + outdir )
+
+end
\ No newline at end of file
--- /dev/null
+# $Id: parameters.rb_dir_qsub,v 1.3 2007/12/20 04:07:13 cmzmasek Exp $
+
+PRG: /home/czmasek/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmpfam
+OPT: -E 20 -A 0 /home/czmasek/DATA/PFAM/Pfam_ls
+SUFFIX: _hmmpfam_22_20_ls
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = pfam2go_reformat
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: pfam2go_reformat.rb,v 1.4 2008/11/27 01:41:36 cmzmasek Exp $
+#
+# Reformat pfam2go to a "association" file suitable as input
+# for microarray GO enrichment/overrepresentation-type analyses,
+# and create a file listing all mapped Pfams as well.
+
+
+module ForesterScripts
+
+ require 'set'
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ if ( ARGV == nil || ARGV.length != 2 )
+ puts( "usage: pfam2go_reformat.rb <pfam2go file> <outfiles base>" )
+ exit( -1 )
+ end
+
+ infile = ARGV[ 0 ]
+ outfilebase = ARGV[ 1 ]
+ outfile_sgd_style = outfilebase + "_sgd_style_associations"
+ outfile_simple_map = outfilebase + "_basic_associations"
+ outfile_all_pfams = outfilebase + "_all_associated_pfams"
+
+ pfams = SortedSet.new
+
+ if ( File.exists?( outfile_sgd_style ) )
+ puts( "outfile [" + outfile_sgd_style + "] already exists" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile_simple_map ) )
+ puts( "outfile [" + outfile_simple_map + "] already exists" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile_all_pfams ) )
+ puts( "outfile [" + outfile_all_pfams + "] already exists" )
+ exit( -1 )
+ end
+ if ( !File.exists?( infile) )
+ puts( "infile [" + infile + "] does not exist" )
+ exit( -1 )
+ end
+
+ out_str_sgd = String.new
+ out_str_basic = String.new
+
+ File.open( infile ) do | file |
+ while line = file.gets
+ if line =~ /^\s*Pfam:PF(\d+)\s+(\S+)\s.+(GO:\d+)\s*$/
+ pfam_id = $1
+ pfam_name = $2
+ go_id = $3
+ new_line = "PFAM" + "\t" + pfam_name + "\t" + pfam_name + "\t\t" + go_id + "\t" + "PF:" + pfam_id + "\t\t\t\t\t\t\t\t\t"
+ out_str_sgd = out_str_sgd + new_line + "\n"
+ out_str_basic = out_str_basic + pfam_name + "\t" + go_id + "\n"
+ pfams.add( pfam_name )
+ end
+ end
+ end
+
+ open( outfile_sgd_style, 'w' ) do |file|
+ file.write( out_str_sgd )
+ end
+ open( outfile_simple_map, 'w' ) do |file|
+ file.write( out_str_basic )
+ end
+ open( outfile_all_pfams, 'w' ) do |file|
+ pfams.each { |pfam|
+ file.write( pfam )
+ file.write( "\n" )
+ }
+ end
+ puts( "number of associated pfams : " + pfams.size.to_s )
+ puts( "wrote assocations in sgd style to : " + outfile_sgd_style )
+ puts( "wrote assocations in basic style to: " + outfile_simple_map )
+ puts( "wrote all associated pfams to : " + outfile_all_pfams )
+ puts( "OK")
+
+end
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = pfam_summarize
+#
+# Copyright:: Copyright (C) 2008-2009 Christian M. Zmasek. All rights reserved.
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: pfam_summarize.rb,v 1.2 2008/08/28 17:09:07 cmzmasek Exp $
+#
+# This extracts ID, AC, DE, TP, and DR values from Pfam data files.
+#
+# Created 2008-06-25 in San Diego, CA, USA by CMZ
+#
+# Usage: pfam_summarize.rb <infile: Pfam data file such as Pfam-A.full> <outfile>
+
+require 'iconv'
+
+module ForesterScripts
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+ SEP = "\t"
+ LINE_DELIMITER = "\n"
+
+ if ( ARGV == nil || ARGV.length != 2 )
+ puts( "usage: pfam_summarize.rb <infile: Pfam data file such as Pfam-A.full> <outfile>" )
+ exit( -1 )
+ end
+
+ pfamfile = ARGV[ 0 ]
+ outfile = ARGV[ 1 ]
+
+ if ( !File.exists?( pfamfile ) )
+ puts( "Pfam data file [" + pfamfile + "] does not exist" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile ) )
+ puts( "outfile [" + outfile + "] already exists" )
+ exit( -1 )
+ end
+
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+
+ id = nil
+ ac = nil
+ de = nil
+ tp = nil
+ dr = Array.new()
+ line_count = 0
+ count = 0
+
+ out = File.open( outfile, 'w' )
+
+ File.open( pfamfile ) do | file |
+ while line = file.gets
+ line_count += 1
+
+ line = ic.iconv( line )
+
+ if ( line =~ /#=GF ID\s+(.+)/ )
+ if ( id != nil )
+ puts( "Pfam data file [" + pfamfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ id = $1
+ elsif ( line =~ /#=GF AC\s+(.+)/ )
+ ac = $1
+ elsif ( line =~ /#=GF DE\s+(.+)/ )
+ de = $1
+ elsif ( line =~ /#=GF TP\s+(.+)/ )
+ tp = $1
+ elsif ( line =~ /#=GF DR\s+(.+)/ )
+ dr.push( $1 )
+ elsif ( line =~ /^\/\// )
+ if ( id == nil || ac == nil )
+ puts( "Pfam data file [" + pfamfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ out.write( id )
+ out.write( SEP )
+ out.write( ac )
+ out.write( SEP )
+ out.write( tp )
+ out.write( SEP )
+ out.write( '[' )
+ out.write( de )
+ out.write( ']' )
+ out.write( SEP )
+ out.write( '[' )
+ dr.each { |d|
+ out.write( d )
+ out.write( ' ' )
+ }
+ out.write( ']' )
+ out.write( LINE_DELIMITER )
+
+ id = nil
+ ac = nil
+ de = nil
+ tp = nil
+ dr = Array.new()
+ count += 1
+ end
+ end
+ end
+
+ out.close
+
+ puts()
+ puts( "Summarized data for " + count.to_s + " individual Pfams to " + outfile )
+ puts( "OK" )
+ puts()
+
+end # module ForesterScripts
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = pfam_to_scop
+#
+# Copyright:: Copyright (C) 2008-2009 Christian M. Zmasek. All rights reserved.
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: pfam_to_scop.rb,v 1.2 2008/08/28 17:09:07 cmzmasek Exp $
+#
+# This extracts ID and SCOP fa (or fa and sf) from Pfam data files.
+#
+# Created 2008-06-25 in San Diego, CA, USA by CMZ
+#
+# Usage: pfam_to_scop.rb <infile: Pfam data file such as Pfam-A.full> <outfile>
+
+require 'iconv'
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ SF = true
+
+ SEP = "\t"
+ LINE_DELIMITER = "\n"
+
+ if ( ARGV == nil || ARGV.length != 2 )
+ puts( "usage: pfam_to_scop.rb <infile: Pfam data file such as Pfam-A.full> <outfile>" )
+ exit( -1 )
+ end
+
+ pfamfile = ARGV[ 0 ]
+ outfile = ARGV[ 1 ]
+
+ if ( !File.exists?( pfamfile ) )
+ puts( "Pfam data file [" + pfamfile + "] does not exist" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile ) )
+ puts( "outfile [" + outfile + "] already exists" )
+ exit( -1 )
+ end
+
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+
+ id = nil
+ scops = Array.new()
+ line_count = 0
+ count = 0
+ scop_count = 0
+
+ out = File.open( outfile, 'w' )
+
+ File.open( pfamfile ) do | file |
+ while line = file.gets
+ line_count += 1
+
+ line = ic.iconv( line )
+
+ if ( line =~ /#=GF ID\s+(.+)/ )
+ if ( id != nil )
+ puts( "Pfam data file [" + pfamfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ id = $1
+ elsif ( line =~ /#=GF\s+DR\s+SCOP;\s+(\w+);\s+fa/ )
+ scops.push( $1 )
+ elsif ( SF && line =~ /#=GF\s+DR\s+SCOP;\s+(\w+);\s+sf/ )
+ scops.push( $1 )
+ elsif ( line =~ /^\/\// )
+ if ( id == nil )
+ puts( "Pfam data file [" + pfamfile + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ scops.each { |s|
+ out.write( id )
+ out.write( SEP )
+ out.write( s )
+ out.write( LINE_DELIMITER )
+ scop_count += 1
+ }
+ id = nil
+ scops = Array.new()
+ count += 1
+ end
+ end
+ end
+
+ out.close
+
+ puts()
+ if ( SF )
+ puts( "Extracted #{scop_count} scop fa and sf identifiers for #{count.to_s} individual Pfams to " + outfile )
+ else
+ puts( "Extracted #{scop_count} scop fa identifiers for #{count.to_s} individual Pfams to " + outfile )
+ end
+ puts( "OK" )
+ puts()
+
+end # module ForesterScripts
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = rb_dir_qsub
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: rb_dir_qsub.rb,v 1.15 2009/11/07 02:06:59 cmzmasek Exp $
+#
+# To execute qsub commands.
+# Submits PRG for every file in the current directory.
+#
+# Examples for PARAMETER_FILE:
+#
+# PRG: /home/user/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmpfam
+# OPT: -E 20 -A 0 /home/user/DATA/PFAM/Pfam_ls
+# SUFFIX: _hmmpfam_22_20_ls
+#
+# PRG: /home/user/SOFTWARE/WUBLAST/tblastn
+# OPT:
+# VOPT: AMPQU
+# VOPT: HYDMA
+# SUFFIX: _blast
+#
+# PRG: /home/czmasek/SOFTWARE/HMMER/hmmer-3.0b2/binaries/intel-linux-x86_64/hmmscan
+# OPT: -E 2 --notextw --qformat fasta /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm
+# SUFFIX: .hmmscan30b2_240
+# OUTPUT: --domtblout
+
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ PARAMETER_FILE = 'parameters.rb_dir_qsub'
+ SLEEP = 1.0
+ REMOVE_SUFFIX = true
+
+ PRG = 'PRG:'
+ OPT = 'OPT:'
+ VOPT = 'VOPT:'
+ OUTPUT_OPT = 'OUTPUT:'
+ SUFFIX = 'SUFFIX:'
+ INPUT_PART = 'INPUT_PART:'
+
+
+ PBS_O_WORKDIR = '$PBS_O_WORKDIR/'
+ TMP_CMD_FILE_SUFFIX = '__QSUB'
+ NAME = 'rb_dir_qsub'
+
+ if ( !File.exists?( PARAMETER_FILE ) )
+ puts( '[' + NAME + '] > parameters file "' + PARAMETER_FILE + '" not found' )
+ Process.exit!
+ end
+ puts( '[' + NAME + '] > reading ' + PARAMETER_FILE )
+
+ prg = ''
+ opt = ''
+ vopts = Array.new
+ suffix = ''
+ input_part = ''
+ output_opt = ''
+ open( PARAMETER_FILE ).each { |line|
+ if ( line.length > 1 && line =~ /^[^#]\S+/ )
+ if line =~ /^#{PRG}\s+(\S+)/
+ prg = $1
+ end
+ if line =~ /^\s*#{OPT}\s+(\S+.+)/
+ opt = $1
+ end
+ if line =~ /^\s*#{VOPT}\s+(\S+.+)/
+ vopts.push( $1 )
+ end
+ if line =~ /^\s*#{SUFFIX}\s+(\S+)/
+ suffix = $1
+ end
+ if line =~ /^\s*#{INPUT_PART}\s+(\S+)/
+ input_part = $1
+ end
+ if line =~ /^\s*#{OUTPUT_OPT}\s+(\S+.+)/
+ output_opt = $1
+ end
+ end
+ }
+ if ( prg.length < 1 )
+ puts( '[' + NAME + '] > no program name found in parameters file "' + PARAMETER_FILE + '"' )
+ Process.exit!
+ end
+ puts( '[' + NAME + '] > program: ' + prg )
+ puts( '[' + NAME + '] > option : ' + opt )
+ vopts.each { |vopt|
+ puts( '[' + NAME + '] > voption: ' + vopt )
+ }
+ puts( '[' + NAME + '] > suffix : ' + suffix )
+ if ( input_part.length > 0 )
+ puts( '[' + NAME + '] > input: ' + input_part )
+ end
+ if ( output_opt.length > 0 )
+ puts( '[' + NAME + '] > output opt : ' + output_opt )
+ end
+ if vopts.empty?
+ vopts.push( "" )
+ end
+
+ files = Dir.entries( "." )
+
+ files.each { |file|
+ if ( !File.directory?( file ) && file !~ /^\./ && file !~ /#{PARAMETER_FILE}/ )
+
+ if ( input_part.length > 0 && file !~ /#{input_part}/ )
+ next
+ end
+ vopts.each { |vopt|
+ cmd = ""
+ outputfile = file.to_str
+ if REMOVE_SUFFIX
+ if outputfile =~ /(.+)\..{1,5}/
+ outputfile = $1
+ end
+ end
+ if output_opt.length > 0
+ cmd = prg + ' ' +
+ output_opt + ' ' + PBS_O_WORKDIR + outputfile + suffix + ' ' +
+ opt + ' ' +
+ PBS_O_WORKDIR + file.to_str +
+ ' > /dev/null'
+ elsif vopt.length > 0
+ cmd = prg + ' ' + opt + ' ' + vopt + ' ' + PBS_O_WORKDIR + file.to_str +
+ ' > ' + PBS_O_WORKDIR + vopt + "_" + outputfile + suffix
+ else
+ cmd = prg + ' ' + opt + ' ' + PBS_O_WORKDIR + file.to_str +
+ ' > ' + PBS_O_WORKDIR + outputfile + suffix
+ end
+ tmp_cmd_file = file.to_str + TMP_CMD_FILE_SUFFIX
+ if File.exists?( tmp_cmd_file )
+ File.delete( tmp_cmd_file )
+ end
+ open( tmp_cmd_file, 'w' ) do |f|
+ f.write( cmd )
+ end
+ puts( '[' + NAME + '] > excuting ' + cmd )
+ IO.popen( 'qsub ' + tmp_cmd_file , 'r+' ) do |pipe|
+ pipe.close_write
+ puts pipe.read
+ end
+ sleep( SLEEP )
+ if File.exists?( tmp_cmd_file )
+ File.delete( tmp_cmd_file )
+ end
+ }
+ end
+ }
+ puts( '[' + NAME + '] > OK.' )
+ puts
+
+end
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = rb_x_qsub
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: rb_dir_x.rb,v 1.8 2008/09/16 23:31:39 cmzmasek Exp $
+#
+# To execute qsub commands.
+# Submits PRG for every file in the current directory.
+#
+# Examples for PARAMETER_FILE:
+#
+# PRG: /home/user/SOFTWARE/HMMER/hmmer-2.3.2/src/hmmpfam
+# OPT: -E 20 -A 0 /home/user/DATA/PFAM/Pfam_ls
+# SUFFIX: _hmmpfam_22_20_ls
+#
+# PRG: /home/user/SOFTWARE/WUBLAST/tblastn
+# OPT:
+# VOPT: AMPQU
+# VOPT: HYDMA
+# SUFFIX: _blast
+
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ PARAMETER_FILE = 'parameters.rb_dir_x'
+ SLEEP = 1.0
+ SPAWN = true
+
+ PRG = 'PRG:'
+ OPT = 'OPT:'
+ VOPT = 'VOPT:'
+ OUTPUT_OPT = 'OUTPUT:' # TODO e.g. > or -o
+ SUFFIX = 'SUFFIX:'
+ INPUT_PART = 'INPUT_PART:'
+
+ NAME = 'rb_dir_x'
+
+ if ( !File.exists?( PARAMETER_FILE ) )
+ puts( '[' + NAME + '] > parameters file "' + PARAMETER_FILE + '" not found' )
+ Process.exit!
+ end
+ puts( '[' + NAME + '] > reading ' + PARAMETER_FILE )
+
+ prg = ''
+ opt = ''
+ vopts = Array.new
+ suffix = ''
+ input_part = ''
+ open( PARAMETER_FILE ).each { |line|
+ if ( line.length > 1 && line =~ /^[^#]\S+/ )
+ if line =~ /^#{PRG}\s+(\S+)/
+ prg = $1
+ end
+ if line =~ /^\s*#{OPT}\s+(\S+.+)/
+ opt = $1
+ end
+ if line =~ /^\s*#{VOPT}\s+(\S+.+)/
+ vopts.push( $1 )
+ end
+ if line =~ /^\s*#{SUFFIX}\s+(\S+)/
+ suffix = $1
+ end
+ if line =~ /^\s*#{INPUT_PART}\s+(\S+)/
+ input_part = $1
+ end
+ end
+ }
+ if ( prg.length < 1 )
+ puts( '[' + NAME + '] > no program name found in parameters file "' + PARAMETER_FILE + '"' )
+ Process.exit!
+ end
+ puts( '[' + NAME + '] > program: ' + prg )
+ puts( '[' + NAME + '] > option : ' + opt )
+ vopts.each { |vopt|
+ puts( '[' + NAME + '] > voption: ' + vopt )
+ }
+ puts( '[' + NAME + '] > suffix : ' + suffix )
+ if ( input_part.length > 0 )
+ puts( '[' + NAME + '] > input : ' + input_part )
+ end
+ if vopts.empty?
+ vopts.push( "" )
+ end
+
+ files = Dir.entries( "." )
+
+ files.each { |file|
+ if ( !File.directory?( file ) && file !~ /^\./ && file !~ /#{PARAMETER_FILE}/ )
+
+ if ( input_part.length > 0 && file !~ /#{input_part}/ )
+ next
+ end
+ vopts.each { |vopt|
+ cmd = ""
+ if vopt.length > 0
+ cmd = 'nohup ' + prg + ' ' + opt + ' ' + vopt + ' ' + file.to_str +
+ ' > ' + vopt + "_" + file.to_str + suffix + ' &'
+ else
+ cmd = 'nohup ' + prg + ' ' + opt + ' ' + file.to_str +
+ ' > ' + file.to_str + suffix + ' &'
+ end
+
+ puts( '[' + NAME + '] > excuting ' + cmd )
+ if SPAWN
+ spawn( cmd, STDERR => "/dev/null" )
+ else
+ IO.popen( cmd , 'r+' ) do |pipe|
+ pipe.close_write
+ puts pipe.read
+ end
+ end
+ sleep( SLEEP )
+
+ }
+ end
+ }
+ puts( '[' + NAME + '] > OK.' )
+ puts
+
+end
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = rb_qsub
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: rb_qsub.rb,v 1.6 2008/08/30 19:57:59 cmzmasek Exp $
+#
+# last modified: 11/13/2007
+#
+#
+# To execute qsub commands.
+# Each line l (unless precded by a # or space) in file
+# 'commands.qsub' is executed as 'qsub l'
+
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ CMDS_FILE = 'commands.qsub'
+ TMP_CMD_FILE = '__QSUB_RB_CMD__'
+ PRG_NAME = 'rb_qsub'
+
+ if ( !File.exists?( CMDS_FILE ) )
+ puts( '[' +PRG_NAME + '] > commands file "' + CMDS_FILE + '" not found' )
+ Process.exit!
+ end
+
+ puts( '[' +PRG_NAME + '] > reading ' + CMDS_FILE )
+
+ open( CMDS_FILE ).each { |line|
+ if ( line.length > 1 && line =~ /^[^#]\S+/ )
+ if ( File.exists?( TMP_CMD_FILE ) )
+ File.delete( TMP_CMD_FILE )
+ end
+ open( TMP_CMD_FILE, 'w' ) do |f|
+ f.write( line )
+ end
+ puts( '[' +PRG_NAME + '] > excuting ' + line )
+ IO.popen( 'qsub ' + TMP_CMD_FILE , 'r+' ) do |pipe|
+ pipe.close_write
+ puts pipe.read
+ end
+ if ( File.exists?( TMP_CMD_FILE ) )
+ File.delete( TMP_CMD_FILE )
+ end
+ sleep( 10.0 )
+ end
+ }
+ puts( '[' +PRG_NAME + '] > OK.' )
+ puts
+
+end
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = replace
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: replace.rb,v 1.5 2008/08/28 17:09:07 cmzmasek Exp $
+#
+# To replace multiple strings in file.
+# Map file contains intructions for replacement (one on each line)
+# in the following format (by example): old#new
+#
+
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ if ( ARGV == nil || ARGV.length != 3 )
+ puts( "usage: replace.rb <map-file> <infile> <outfile>" )
+ exit( -1 )
+ end
+ mapfile = ARGV[ 0 ]
+ infile = ARGV[ 1 ]
+ outfile = ARGV[ 2 ]
+
+
+ if ( File.exists?( outfile ) )
+ puts( "outfile [" + outfile + "] already exists" )
+ exit( -1 )
+ end
+ if ( !File.exists?( infile) )
+ puts( "infile [" + infile + "] does not exist" )
+ exit( -1 )
+ end
+ if ( !File.exists?( mapfile ) )
+ puts( "mapfile [" + mapfile + "] does not exist" )
+ exit( -1 )
+ end
+
+ old_new_map = Hash.new
+
+ File.open( mapfile ) do | file |
+ while line = file.gets
+ if ( line =~/(\S+)\s*#\s*(\S+)/ )
+ old_new_map[ $1 ] = $2
+ puts( $1 + ' => ' + $2 )
+ end
+ end
+ end
+
+ if ( old_new_map.size < 1 )
+ puts( "mapping file was empty" )
+ exit( -1 )
+ end
+
+ data_str = String.new
+
+ File.open( infile ) do | file |
+ while line = file.gets
+ data_str = data_str + line.chomp
+ end
+ end
+
+ old_new_map.each_pair{ |old, new|
+ data_str = data_str.gsub( old, new )
+ }
+
+ open( outfile, 'w' ) do |file|
+ file.write( data_str )
+ end
+
+ puts( "wrote " + outfile )
+
+end
+
+
\ No newline at end of file
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = replace_id
+#
+# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: replace_id.rb,v 1.8 2008/08/28 17:09:07 cmzmasek Exp $
+#
+# To replace ()by way of example '123_CHI5' with '123_CHICK5'
+# given a mapping file containing '123_CHICKEN'
+# (in the form '123_CHICKEN: some description which is ignored').
+#
+# Note. This will break if the species id ends with a number (as is
+# in the case for many bacteria).
+
+
+module ForesterScripts
+
+if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ NUMBER_OF_LETTERS = 3
+
+ if ( ARGV == nil || ARGV.length != 3 )
+ puts( "usage: replace_id.rb <map-file> <infile> <outfile>" )
+ exit( -1 )
+ end
+ mapfile = ARGV[ 0 ]
+ infile = ARGV[ 1 ]
+ outfile = ARGV[ 2 ]
+
+
+ if ( File.exists?( outfile ) )
+ puts( "outfile [" + outfile + "] already exists" )
+ exit( -1 )
+ end
+ if ( !File.exists?( infile) )
+ puts( "infile [" + infile + "] does not exist" )
+ exit( -1 )
+ end
+ if ( !File.exists?( mapfile ) )
+ puts( "mapfile [" + mapfile + "] does not exist" )
+ exit( -1 )
+ end
+
+ number_to_complete_id_map = Hash.new
+
+ File.open( mapfile ) do | file |
+ while line = file.gets
+ if ( line =~ /(\d+_\S+)\s*:/ )
+ complete_id = $1
+ complete_id =~ /(\d+)_\S+/
+ number_to_complete_id_map[ $1 ] = complete_id
+ puts( $1 + ' => ' + complete_id )
+ end
+ end
+ end
+
+ if ( number_to_complete_id_map.size < 1 )
+ puts( "mapping file was empty" )
+ exit( -1 )
+ end
+
+ data_str = String.new
+
+ File.open( infile ) do | file |
+ while line = file.gets
+ data_str = data_str + line.chomp
+ end
+ end
+
+ replacements = 0
+ number_to_complete_id_map.each_pair{ |number, id|
+ data_str.gsub!( /\b#{number}_[A-Z]{#{NUMBER_OF_LETTERS}}/, id )
+ }
+
+ open( outfile, 'w' ) do |file|
+ file.write( data_str )
+ end
+
+ puts( "wrote " + outfile )
+ puts( "OK" )
+
+end
+
--- /dev/null
+#!/usr/local/bin/ruby -w
+#
+# = scoptastic
+#
+# Copyright:: Copyright (C) 2008-2009 Christian M. Zmasek.
+# All rights reserved.
+# License:: GNU Lesser General Public License (LGPL)
+#
+# $Id: scoptastic.rb,v 1.3 2008/08/28 17:09:07 cmzmasek Exp $
+#
+# To create Pfam id to SCOP mappings, one for each of four levels of SCOP
+# classification.
+#
+# Created 2008-06-25 in San Diego, CA, USA by CMZ
+#
+# Usage: scoptastic.rb scoptastic.rb <Pfam id to ac map file, e.g.
+# pfam_summarize.rb output> <Pfam ac to SCOP classification map file> <Pfam id
+# to SCOP outfile root>
+
+
+require 'iconv'
+
+module ForesterScripts
+
+ if RUBY_VERSION !~ /1.9/
+ puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+ exit( -1 )
+ end
+
+ CLASS_LEVEL_SUFFIX = "_SCOP_2_CLASS"
+ FOLD_LEVEL_SUFFIX = "_SCOP_3_FOLD"
+ SUPERFAMILY_LEVEL_SUFFIX = "_SCOP_4_SUPERFAMILY"
+ FAMILY_LEVEL_SUFFIX = "_SCOP_5_FAMILY"
+
+ SEP = "\t"
+ LINE_DELIMITER = "\n"
+
+ if ( ARGV == nil || ARGV.length != 3 )
+ puts( "usage: scoptastic.rb <Pfam id to ac map file, e.g. pfam_summarize.rb output> <Pfam ac to SCOP classification map file> <Pfam id to SCOP outfile root>" )
+ exit( -1 )
+ end
+
+ pfam_id_to_ac = ARGV[ 0 ]
+ pfam_ac_to_scop = ARGV[ 1 ]
+ outfile = ARGV[ 2 ]
+
+ if ( !File.exists?( pfam_id_to_ac ) )
+ puts( "Pfam id to ac map file [" + pfam_id_to_ac + "] does not exist" )
+ exit( -1 )
+ end
+ if ( !File.exists?( pfam_ac_to_scop ) )
+ puts( "Pfam ac to SCOP classification map file [" + pfam_ac_to_scop + "] does not exist" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile + CLASS_LEVEL_SUFFIX ) )
+ puts( "Outfile [" + outfile + CLASS_LEVEL_SUFFIX + "] already exists" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile + FOLD_LEVEL_SUFFIX ) )
+ puts( "Outfile [" + outfile + FOLD_LEVEL_SUFFIX + "] already exists" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile + SUPERFAMILY_LEVEL_SUFFIX ) )
+ puts( "Outfile [" + outfile + SUPERFAMILY_LEVEL_SUFFIX + "] already exists" )
+ exit( -1 )
+ end
+ if ( File.exists?( outfile + FAMILY_LEVEL_SUFFIX ) )
+ puts( "Outfile [" + outfile + FAMILY_LEVEL_SUFFIX + "] already exists" )
+ exit( -1 )
+ end
+
+ ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
+
+ pfam_ac_to_id_map = Hash.new
+
+ pfam_ac_to_scop_map = Hash.new
+
+ count = 0
+
+ File.open( pfam_id_to_ac ) do | file |
+ while line = file.gets
+ line = ic.iconv( line )
+ if ( line !~ /^#/ && line =~ /\S/ )
+ if ( line =~ /^(\S+)\s+(PF\d+)/ )
+ pfam_ac_to_id_map[ $2 ] = $1
+ count += 1
+ else
+ puts( "Pfam id to ac map file [" + pfam_id_to_ac + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ end
+ end
+ end
+ puts()
+ puts( "Extracted #{count} Pfam id to ac mappings from file [#{pfam_id_to_ac}]" )
+
+ count = 0
+ File.open( pfam_ac_to_scop ) do | file |
+ while line = file.gets
+ line = ic.iconv( line )
+ if ( line !~ /^#/ && line =~ /\S/ )
+ if ( line =~ /^(PF\d+)\.?\d*\s+([a-z]\.\d+\.\d+\.\d+)/ )
+ pfam_ac_to_scop_map[ $1 ] = $2
+ count += 1
+ else
+ puts( "Pfam ac to SCOP classification map file [" + pfam_ac_to_scop + "] format error [line: " + line + "]" )
+ exit( -1 )
+ end
+ end
+ end
+ end
+
+ puts( "Extracted #{count} Pfam ac to SCOP classification mappings from file [#{pfam_ac_to_scop}]" )
+
+ out_class_level = File.open( outfile + CLASS_LEVEL_SUFFIX, 'w' )
+ out_fold_level = File.open( outfile + FOLD_LEVEL_SUFFIX , 'w' )
+ out_superfamily_level = File.open( outfile + SUPERFAMILY_LEVEL_SUFFIX, 'w' )
+ out_family_level = File.open( outfile + FAMILY_LEVEL_SUFFIX, 'w' )
+
+ count = 0
+ pfam_ac_to_scop_map.each { | pfam_ac,scop |
+ if ( pfam_ac_to_id_map.has_key?( pfam_ac ) )
+ pfam_id = pfam_ac_to_id_map[ pfam_ac ]
+ scop_split = scop.split( "\." )
+
+ out_class_level.write( pfam_id )
+ out_fold_level.write( pfam_id )
+ out_superfamily_level.write( pfam_id )
+ out_family_level.write( pfam_id )
+
+ out_class_level.write( SEP )
+ out_fold_level.write( SEP )
+ out_superfamily_level.write( SEP )
+ out_family_level.write( SEP )
+
+ out_class_level.write( scop_split[ 0 ] )
+ out_fold_level.write( scop_split[ 0 ] + "." + scop_split[ 1 ] )
+ out_superfamily_level.write( scop_split[ 0 ] + "." + scop_split[ 1 ] + "." + scop_split[ 2 ] )
+ out_family_level.write( scop )
+
+ out_class_level.write( LINE_DELIMITER )
+ out_fold_level.write( LINE_DELIMITER )
+ out_superfamily_level.write( LINE_DELIMITER )
+ out_family_level.write( LINE_DELIMITER )
+ count += 1
+ else
+ puts( "Pfam ac #{pfam_ac} not found in Pfam id to ac map file [" + pfam_id_to_ac + "]" )
+ exit( -1 )
+ end
+ }
+
+ out_class_level.close
+ out_fold_level.close
+ out_superfamily_level.close
+ out_family_level.close
+
+ puts()
+ puts( "Wrote #{count} Pfam id to SCOP mappings to files '#{outfile + CLASS_LEVEL_SUFFIX}', '#{outfile + FOLD_LEVEL_SUFFIX}', '#{outfile + SUPERFAMILY_LEVEL_SUFFIX}', and '#{ outfile + FAMILY_LEVEL_SUFFIX}'" )
+ puts( "OK" )
+ puts()
+
+end # module ForesterScripts
+
git://source.jalview.org / jalview.git / commitdiff