#
# = 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 $
-
+# Copyright:: Copyright (C) 2017 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
+require 'lib/evo/util/constants'
require 'lib/evo/util/util'
require 'lib/evo/msa/msa_factory'
require 'lib/evo/msa/msa'
require 'lib/evo/util/command_line_arguments'
module Evoruby
-
class TaxonomyProcessor
PRG_NAME = "tap"
- PRG_DATE = "2012.09.27"
- PRG_DESC = "replacement of species names in multiple sequence files"
- PRG_VERSION = "1.02"
- COPYRIGHT = "2012 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
-
- SIMPLE = false
+ PRG_DATE = "170214"
+ PRG_DESC = "Replacement of labels in multiple sequence files"
+ PRG_VERSION = "2.004"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
EXTRACT_TAXONOMY_OPTION = "t"
-
- def initialize()
- @taxonomies = Hash.new()
- end
-
+ ANNOTATION_OPTION = "a"
+ 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 ( ARGV == nil || ( ARGV.length != 1 && ARGV.length != 2 && 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()
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ( ARGV.length < 1 ) )
+ print_help()
exit( -1 )
end
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
- mapfile = nil
- input = nil
- output = nil
- list_file = 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
+ if 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 )
else
i = input
end
- output = i + "_ni.fasta"
- list_file = i + ".nim"
+ output = i + Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX
+ list_file = i + Constants::ID_MAP_FILE_SUFFIX
+ else
+ print_help()
+ exit(-1)
end
-
allowed_opts = Array.new
allowed_opts.push( EXTRACT_TAXONOMY_OPTION )
+ allowed_opts.push( ANNOTATION_OPTION )
disallowed = cla.validate_allowed_options_as_str( allowed_opts )
if ( disallowed.length > 0 )
extract_taxonomy = true
end
- if ( File.exists?( output ) )
+ annotation = nil
+ if ( cla.is_option_set?( ANNOTATION_OPTION ) )
+ annotation = cla.get_option_value( ANNOTATION_OPTION )
+ end
+
+ if ( File.exist?( output ) )
Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" )
end
- if ( File.exists?( list_file ) )
+ if ( File.exist?( list_file ) )
Util.fatal_error( PRG_NAME, "list file [" + list_file + "] already exists" )
end
- if ( !File.exists?( input) )
+ if ( !File.exist?( 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 ( 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
+ if ( annotation != nil )
+ puts( "Annotation : " + annotation )
end
+ puts()
f = MsaFactory.new()
begin
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 ) )
+ seq = msa.get_sequence( i )
+ seq.set_name( modify_name( seq.get_name(), i, lf, extract_taxonomy, annotation ) )
end
-
io = MsaIO.new()
w = nil
if ( fasta_like )
else
w = PhylipSequentialWriter.new()
end
- w.set_max_name_length( 10 )
+ w.set_max_name_length( 9 )
w.clean( true )
begin
io.write_to_file( msa, output, w )
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, "next steps in standard analysis pipeline: hmmscan followed by hsp.rb")
Util.print_message( PRG_NAME, "OK" )
end
private
- def modify_name( desc, counter, file, species_map, extract_taxonomy )
+ def modify_name( desc, counter, file, extract_taxonomy, annotation )
new_desc = nil
- my_species = nil
- # if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/
- desc.gsub!( /:\s+/, ":" ) #new
- desc.gsub!( /\s+/, " " ) #new
- if desc =~ /^>?\s*\S{1,10}_([A-Z]{3,5})/
- new_desc = counter.to_s( 16 ) + "_" + $1
- elsif SIMPLE
- new_desc = counter.to_s( 16 )
- elsif extract_taxonomy
-
- 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 =~/.*\[(\S{3,}?)\]/
- if desc =~/\[([A-Z0-9]{3,6})\]\s*$/ #new
- 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 )
+ desc.gsub!( /\s+/, ' ' )
+ if extract_taxonomy
+ if desc =~/\s\[(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)\]/
+ new_desc = counter.to_s( 16 ) + "_" + $1
else
- new_desc = counter.to_s( 16 ) + "_" + species
+ Util.fatal_error( PRG_NAME, "could not get taxonomy from: " + desc )
end
+ else
+ new_desc = counter.to_s( 16 )
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" )
+ if (annotation != nil)
+ new_desc = new_desc + annotation
+ file.print( new_desc + "\t" + desc + " " + annotation + "\n" )
else
- file.print( new_desc + ": " + desc + "\n" )
+ file.print( new_desc + "\t" + desc + "\n" )
+ end
+ if ( new_desc.length > 9)
+ Util.fatal_error( PRG_NAME, "shortened identifier [" +
+ new_desc + "] is too long (" + new_desc.length.to_s + " characters)" )
end
new_desc
end
+ def print_help()
+ puts( "Usage:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb [options] <input sequences> [output sequences] [output id list]" )
+ puts()
+ puts( " options: -" + EXTRACT_TAXONOMY_OPTION + " : to extract taxonomy information from bracketed expressions" )
+ puts( " -" + ANNOTATION_OPTION + "=<s>: to add an annotation to all entries" )
+ puts()
+ puts( " [next steps in standard analysis pipeline: hmmscan followed by hsp.rb]")
+ puts()
+ puts( "Example:" )
+ puts()
+ puts( " " + PRG_NAME + ".rb P53.fasta" )
+ puts()
+ end
+
end # class TaxonomyProcessor
end # module Evoruby
git://source.jalview.org / jalview.git / blobdiff