From: cmzmasek@gmail.com Date: Sat, 14 Jul 2012 00:09:11 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=262c382b0cc17048d8a283246a9613c8077eeb02;p=jalview.git in progress --- diff --git a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb index 8e6dabd..c8a0e54 100644 --- a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb @@ -37,7 +37,6 @@ module Evoruby FASTA_WITH_NORMALIZED_IDS_SUFFIX = ".ni.fasta" NORMALIZED_IDS_MAP_SUFFIX = ".nim" PROTEINS_LIST_FILE_SEPARATOR = "\t" - CACHE_GENOMES = false def run() @@ -64,7 +63,7 @@ module Evoruby exit( 0 ) end - if ( cla.get_number_of_files != 3 && cla.get_number_of_files != 4 ) + if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 ) print_help exit( -1 ) end @@ -81,10 +80,11 @@ module Evoruby seq_names_files_suffix = cla.get_file_name( 0 ) input_dir = cla.get_file_name( 1 ) out_dir = cla.get_file_name( 2 ) + out_dir_doms = cla.get_file_name( 3 ) mapping_file = nil - if ( cla.get_number_of_files == 4 ) - mapping_file = cla.get_file_name( 3 ) + if ( cla.get_number_of_files == 5 ) + mapping_file = cla.get_file_name( 4 ) begin Util.check_file_for_readability( mapping_file ) rescue ArgumentError => e @@ -98,12 +98,18 @@ module Evoruby if !File.exist?( out_dir ) Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" ) end + if !File.exist?( out_dir_doms ) + Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] 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 + if !File.directory?( out_dir_doms ) + Util.fatal_error( PRG_NAME, "error: [#{out_dir_doms}] is not a directory" ) + end log = String.new @@ -119,6 +125,8 @@ module Evoruby log << "Input dir : " + input_dir + ld puts( "Output dir : " + out_dir ) log << "Output dir : " + out_dir + ld + puts( "Output dir domains : " + out_dir_doms ) + log << "Output dir domains : " + out_dir_doms + ld if ( mapping_file != nil ) puts( "Mapping file : " + mapping_file ) log << "Mapping file : " + mapping_file + ld @@ -147,6 +155,7 @@ module Evoruby species_to_genomes, log, out_dir, + out_dir_doms, mapping_file ) } puts @@ -163,6 +172,7 @@ module Evoruby species_to_genomes, log, out_dir, + out_dir_doms, mapping_file ) begin @@ -170,15 +180,16 @@ module Evoruby 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 + doms_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + FASTA_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 ) + Util.check_file_for_writability( doms_out_file_path_fasta_file ) rescue ArgumentError => e Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end @@ -194,6 +205,7 @@ module Evoruby current_msa = nil new_msa = Msa.new new_msa_normalized_ids = Msa.new + new_msa_domains = Msa.new per_species_counter = 0 puts basename @@ -202,6 +214,7 @@ module Evoruby 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 @@ -210,6 +223,11 @@ module Evoruby next end seq_name = values[ 1 ] + domain_ranges = nil + if ( values.length > 2 ) + domain_ranges_block = values[ 2 ] + domain_ranges = domain_ranges_block.split( "/" ) + end if ( species != current_species ) current_species = species my_file = input_dir + Constants::FILE_SEPARATOR + current_species @@ -227,14 +245,7 @@ module Evoruby 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 + current_msa = read_fasta_file( my_file ) end if ( per_species_counter > 0 ) @@ -271,13 +282,27 @@ module Evoruby ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER ) + orig_name = nil if ( seq != nil ) + orig_name = seq.get_name 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 + if domain_ranges != nil + domain_ranges.each { |range| + if range != nil + s= range.split("-") + from = s[ 0 ] + to = s[ 1 ] + puts from + "-" + to + new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from..to] ) ) + end + } + end + new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) ) end @@ -303,6 +328,14 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end + if new_msa_domains != nil + begin + io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer ) + rescue Exception => e + Util.fatal_error( PRG_NAME, "error: " + e.to_s ) + end + end + begin io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer ) rescue Exception => e @@ -387,10 +420,10 @@ module Evoruby puts( "Usage:" ) puts() puts( " " + PRG_NAME + ".rb [mapping file for " + + "and possibly genome multiple-sequence ('fasta') files> [mapping file for " + "genome multiple-sequence ('fasta') files not in input dir]" ) puts() - puts( " " + "Example: \"mse.rb .prot . seqs ../genome_locations.txt\"" ) + puts( " " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" ) puts() end