+++ /dev/null
-#
-# = lib/evo/apps/domain_sequence_extractor.rb - DomainSequenceExtractor class
-#
-# Copyright:: Copyright (C) 2012 Christian M. Zmasek
-# License:: GNU Lesser General Public License (LGPL)
-#
-# $Id:Exp $
-
-
-require 'lib/evo/util/constants'
-require 'lib/evo/util/util'
-require 'lib/evo/util/command_line_arguments'
-require 'lib/evo/io/parser/hmmscan_domain_extractor'
-
-module Evoruby
-
- class DomainSequenceExtractor
-
- PRG_NAME = "dsx"
- PRG_VERSION = "1.000"
- PRG_DESC = "extraction of domain sequences from hmmscan output"
- PRG_DATE = "20120906"
- COPYRIGHT = "2012 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'
- ADD_SPECIES = 's'
- 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 != 4 )
- 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 )
- allowed_opts.push( ADD_SPECIES )
-
- disallowed = cla.validate_allowed_options_as_str( allowed_opts )
- if ( disallowed.length > 0 )
- Util.fatal_error( PRG_NAME,
- "unknown option(s): " + disallowed,
- STDOUT )
- end
-
- domain_id = cla.get_file_name( 0 )
- hmmsearch_output = cla.get_file_name( 1 )
- fasta_sequence_file = cla.get_file_name( 2 )
- outfile = cla.get_file_name( 3 )
-
- 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
-
- add_species = false
- if cla.is_option_set? ADD_SPECIES
- add_species = 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( "Domain : " + domain_id )
- log << "Domain : " + domain_id + ld
- puts( "Hmmscan outputfile : " + hmmsearch_output )
- log << "Hmmscan 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 = HmmscanDomainExtractor.new()
- domain_count = parser.parse( domain_id,
- 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,
- add_species,
- 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] <domain> <hmmscan 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( " -" + ADD_SPECIES + ": to add species [in brackets]" )
- puts()
- end
-
- end # class DomainSequenceExtractor
-
-end # module Evoruby
git://source.jalview.org / jalview.git / commitdiff