2 # = lib/evo/apps/multi_sequence_extractor.rb - MultiSequenceExtractor class
4 # Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
7 # $Id: multi_sequence_extractor.rb,v 1.10 2010/12/13 19:00:11 cmzmasek Exp $
10 require 'lib/evo/util/constants'
11 require 'lib/evo/util/util'
12 require 'lib/evo/msa/msa'
13 require 'lib/evo/msa/msa_factory'
14 require 'lib/evo/io/msa_io'
15 require 'lib/evo/io/parser/fasta_parser'
16 require 'lib/evo/io/writer/fasta_writer'
17 require 'lib/evo/util/command_line_arguments'
23 class MultiSequenceExtractor
27 PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
28 PRG_DATE = "2008.08.13"
29 COPYRIGHT = "2008-2009 Christian M Zmasek"
30 CONTACT = "phylosoft@gmail.com"
31 WWW = "www.phylosoft.org"
32 HELP_OPTION_1 = 'help'
35 LOG_SUFFIX = ".mse_log"
36 FASTA_SUFFIX = ".fasta"
37 FASTA_WITH_NORMALIZED_IDS_SUFFIX = ".ni.fasta"
38 NORMALIZED_IDS_MAP_SUFFIX = ".nim"
39 PROTEINS_LIST_FILE_SEPARATOR = "\t"
43 Util.print_program_information( PRG_NAME,
52 ld = Constants::LINE_DELIMITER
55 cla = CommandLineArguments.new( ARGV )
56 rescue ArgumentError => e
57 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
60 if ( cla.is_option_set?( HELP_OPTION_1 ) ||
61 cla.is_option_set?( HELP_OPTION_2 ) )
66 if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
71 allowed_opts = Array.new
73 disallowed = cla.validate_allowed_options_as_str( allowed_opts )
74 if ( disallowed.length > 0 )
75 Util.fatal_error( PRG_NAME,
76 "unknown option(s): " + disallowed,
80 seq_names_files_suffix = cla.get_file_name( 0 )
81 input_dir = cla.get_file_name( 1 )
82 out_dir = cla.get_file_name( 2 )
83 out_dir_doms = cla.get_file_name( 3 )
86 if ( cla.get_number_of_files == 5 )
87 mapping_file = cla.get_file_name( 4 )
89 Util.check_file_for_readability( mapping_file )
90 rescue ArgumentError => e
91 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
95 if !File.exist?( input_dir )
96 Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
98 if !File.exist?( out_dir )
99 Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
101 if !File.exist?( out_dir_doms )
102 Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" )
104 if !File.directory?( input_dir )
105 Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
107 if !File.directory?( out_dir )
108 Util.fatal_error( PRG_NAME, "error: [#{out_dir}] is not a directory" )
110 if !File.directory?( out_dir_doms )
111 Util.fatal_error( PRG_NAME, "error: [#{out_dir_doms}] is not a directory" )
117 log << "Program : " + PRG_NAME + ld
118 log << "Version : " + PRG_VERSION + ld
119 log << "Program date : " + PRG_DATE + ld
122 puts( "Sequence names files suffix: " + seq_names_files_suffix )
123 log << "Sequence names files suffix: " + seq_names_files_suffix + ld
124 puts( "Input dir : " + input_dir )
125 log << "Input dir : " + input_dir + ld
126 puts( "Output dir : " + out_dir )
127 log << "Output dir : " + out_dir + ld
128 puts( "Output dir domains : " + out_dir_doms )
129 log << "Output dir domains : " + out_dir_doms + ld
130 if ( mapping_file != nil )
131 puts( "Mapping file : " + mapping_file )
132 log << "Mapping file : " + mapping_file + ld
134 log << "Date : " + Time.now.to_s + ld
137 if ( mapping_file != nil )
138 species_codes_to_paths = extract_mappings( mapping_file )
141 input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
144 species_to_genomes = Hash.new()
146 input_files.each { |input_file|
150 puts counter.to_s + "/" + input_files.size.to_s
151 read_seq_family_file( input_file,
152 seq_names_files_suffix,
154 species_codes_to_paths,
162 Util.print_message( PRG_NAME, "OK" )
168 def read_seq_family_file( input_file,
169 seq_names_files_suffix,
171 species_codes_to_paths,
179 Util.check_file_for_readability( input_file )
180 rescue ArgumentError => e
181 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
183 basename = File.basename( input_file, seq_names_files_suffix )
184 out_file_path_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
185 out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
186 out_file_path_ids_map = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
187 doms_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
189 Util.check_file_for_writability( out_file_path_fasta_file )
190 Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
191 Util.check_file_for_writability( out_file_path_ids_map )
192 Util.check_file_for_writability( doms_out_file_path_fasta_file )
193 rescue ArgumentError => e
194 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
199 ids_map_writer = File.open( out_file_path_ids_map, 'a' )
200 rescue Exception => e
201 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
207 new_msa_normalized_ids = Msa.new
208 new_msa_domains = Msa.new
209 per_species_counter = 0
213 File.open( input_file ) do | file |
214 while line = file.gets
215 if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
216 values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
218 if ( values.length < 2 )
219 Util.fatal_error( PRG_NAME, "unexpected format: " + line )
221 species = values[ 0 ]
222 if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
225 seq_name = values[ 1 ]
227 if ( values.length > 2 )
228 domain_ranges_block = values[ 2 ]
229 domain_ranges = domain_ranges_block.split( "/" )
231 if ( species != current_species )
232 current_species = species
233 my_file = input_dir + Constants::FILE_SEPARATOR + current_species
235 if ( !File.exist?( my_file ) )
236 if species_codes_to_paths == nil
237 Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
238 elsif ( !species_codes_to_paths.has_key?( current_species ) )
239 Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
241 my_file = species_codes_to_paths[ current_species ]
243 my_path = File.expand_path( my_file )
244 my_readlink = my_path
245 if ( File.symlink?( my_path ) )
246 my_readlink = File.readlink( my_path )
248 current_msa = read_fasta_file( my_file )
251 if ( per_species_counter > 0 )
252 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
253 per_species_counter = 0
255 puts " " + current_species + " [" + my_readlink + "]"
256 log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
259 log << " " + seq_name + Constants::LINE_DELIMITER
260 per_species_counter = per_species_counter + 1
263 if current_msa.find_by_name_start( seq_name, true ).size > 0
265 seq = current_msa.get_by_name_start( seq_name, true ).copy
266 rescue ArgumentError => e
267 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
270 # Not found, try finding by partial match.
272 seq = current_msa.get_by_name( seq_name, true, true )
273 rescue ArgumentError => e
274 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
278 normalized_id = per_species_counter.to_s( 16 ).upcase +
279 "_" + current_species
281 per_species_counter.to_i
283 ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
287 orig_name = seq.get_name
288 seq.set_name( seq.get_name + " [" + current_species + "]" )
289 new_msa.add_sequence( seq )
291 Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
294 if domain_ranges != nil
295 domain_ranges.each { |range|
301 new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from..to] ) )
306 new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
315 if ( per_species_counter > 0 )
316 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
321 fasta_writer = FastaWriter.new()
322 fasta_writer.remove_gap_chars
326 io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
327 rescue Exception => e
328 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
331 if new_msa_domains != nil
333 io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer )
334 rescue Exception => e
335 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
340 io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
341 rescue Exception => e
342 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
346 f = File.open( out_dir + Constants::FILE_SEPARATOR + basename + LOG_SUFFIX , 'a' )
349 rescue Exception => e
350 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
355 def obtain_inputfiles( input_dir, seq_names_files_suffix )
356 input_files = Array.new()
357 Dir.foreach( input_dir ) { |file_name|
358 if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
359 input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
365 def extract_mappings( mapping_file )
366 species_code_to_path = Hash.new()
367 File.open( mapping_file ) do | file |
368 while line = file.gets
369 if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
370 if ( line =~ /(\S+)\s+(\S+)/ )
373 if ( species_code_to_path.has_key?( species ) )
374 Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
376 if ( species_code_to_path.has_value?( path ) )
377 Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
379 if ( !File.exist?( path ) )
380 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
382 if ( !File.file?( path ) )
383 Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
385 if ( !File.readable?( path ) )
386 Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
388 if ( File.size( path ) < 10000 )
389 Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
391 if ( !Util.looks_like_fasta?( path ) )
392 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
394 species_code_to_path[ species ] = path
395 puts species + " -> " + path
403 def print_counts( per_species_counter, log, ld )
404 puts " [sum: " + per_species_counter.to_s + "]"
405 log << " [sum: " + per_species_counter.to_s + "]" + ld
408 def read_fasta_file( input )
412 msa = f.create_msa_from_file( input, FastaParser.new() )
413 rescue Exception => e
414 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
422 puts( " " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
423 "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
424 "genome multiple-sequence ('fasta') files not in input dir]" )
426 puts( " " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" )
430 end # class MultiSequenceExtractor