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"
-
- 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 )
+ 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"
+
+ 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 != 4 && cla.get_number_of_files != 5 )
+ 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 )
+ out_dir_doms = cla.get_file_name( 3 )
+ mapping_file = nil
+
+ 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
+ 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.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
+
+ 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
+ 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
+ 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
+
+ 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,
+ log,
+ out_dir,
+ out_dir_doms,
+ 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,
+ log,
+ out_dir,
+ out_dir_doms,
+ 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
+ doms_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains" + 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
+
+ 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
+ new_msa_domains = 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
-
- if ( cla.is_option_set?( HELP_OPTION_1 ) ||
- cla.is_option_set?( HELP_OPTION_2 ) )
- print_help
- exit( 0 )
+ species = values[ 0 ]
+ if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
+ next
end
-
- if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
- 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 )
+ seq_name = values[ 1 ]
+ domain_ranges = nil
+ if ( values.length > 3 )
+ domain_ranges_block = values[ 3 ]
+ domain_ranges = domain_ranges_block.split( "/" )
end
-
- 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 == 5 )
- mapping_file = cla.get_file_name( 4 )
- begin
- Util.check_file_for_readability( mapping_file )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ 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 = read_fasta_file( my_file )
+
+ 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
-
- 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.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" )
+ 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
+ else
+ # 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
- 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
- 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
+ per_species_counter.to_i
+
+ 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
- log << "Date : " + Time.now.to_s + ld
- puts
- if ( mapping_file != nil )
- species_codes_to_paths = extract_mappings( mapping_file )
+ if domain_ranges != nil
+ domain_ranges.each { |range|
+ if range != nil && range.length > 0
+ s= range.split("-")
+ from = s[ 0 ]
+ to = s[ 1 ]
+ new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from.to_i..to.to_i] ) )
+ end
+ }
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,
- out_dir_doms,
- mapping_file )
- }
- puts
- Util.print_message( PRG_NAME, "OK" )
- puts
+ new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
+ end
end
+ end
- def read_seq_family_file( input_file,
- seq_names_files_suffix,
- input_dir,
- species_codes_to_paths,
- species_to_genomes,
- log,
- out_dir,
- out_dir_doms,
- 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
- 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
-
- 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
- new_msa_domains = 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 ]
- if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
- next
- end
- seq_name = values[ 1 ]
- domain_ranges = nil
- if ( values.length > 3 )
- domain_ranges_block = values[ 3 ]
- puts "domain_ranges_bloc=" + domain_ranges_block
- domain_ranges = domain_ranges_block.split( "/" )
- end
- 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 = read_fasta_file( my_file )
-
-
- 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 )
-
- 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|
- puts "reange:" + range + ":\n"
- if range != nil && range.length > 0
- 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_i..to.to_i] ) )
- end
- }
- 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()
+ ids_map_writer.close
- 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
-
- 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
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
- end
+ if ( per_species_counter > 0 )
+ print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
+ 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
+ io = MsaIO.new()
- end
+ fasta_writer = FastaWriter.new()
+ fasta_writer.remove_gap_chars
+ fasta_writer.clean
- 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
+ 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
- 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
+ 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
-
- def print_counts( per_species_counter, log, ld )
- puts " [sum: " + per_species_counter.to_s + "]"
- log << " [sum: " + per_species_counter.to_s + "]" + ld
+ 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
-
- 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 )
+ }
+ 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
- msa
+ end
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 for sequences> <output directory for domains> [mapping file for " +
- "genome multiple-sequence ('fasta') files not in input dir]" )
- puts()
- puts( " " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" )
- puts()
- end
-
- end # class MultiSequenceExtractor
+ 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 for sequences> <output directory for domains> [mapping file for " +
+ "genome multiple-sequence ('fasta') files not in input dir]" )
+ puts()
+ puts( " " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" )
+ puts()
+ end
+
+ end # class MultiSequenceExtractor
end
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff