2 # = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
4 # Copyright:: Copyright (C) 2012 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
10 require 'lib/evo/util/constants'
11 require 'lib/evo/msa/msa_factory'
12 require 'lib/evo/io/msa_io'
13 require 'lib/evo/io/writer/fasta_writer'
14 require 'lib/evo/io/parser/fasta_parser'
19 class HmmscanDomainExtractor
27 def process_hmmscan_datas( hmmscan_datas,
37 actual_out_of = hmmscan_datas.size
39 domain_pass_counter = 0;
41 hmmscan_datas.each_with_index do |hmmscan_data, index|
42 if hmmscan_data.number < ( index + 1 )
43 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
44 raise StandardError, error_msg
47 extract_domain( hmmscan_data.seq_name,
50 hmmscan_data.env_from,
58 domain_pass_counter += 1
60 if passed_seqs.find_by_name_start( hmmscan_data.seq_name, true ).length < 1
61 add_sequence( hmmscan_data.seq_name, in_msa, passed_seqs )
65 extract_domain( hmmscan_data.seq_name,
68 hmmscan_data.env_from,
78 if (( first && next_env_from - env_to >= min_linker )
80 ( last && env_from - prev_env_to >= min_linker )
82 ( !first && !last && ( next_env_from - env_to >= min_linker ) && ( last && env_from - prev_env_to >= min_linker ) ))
86 elsif !first && ( env_from - prev_env_to ) <= min_linker
87 extract_domain( sequence,
88 prev_number.to_s + "+" + number.to_s,
106 extract_domain( sequence,
119 singlets_counter += 1
121 if sequence != prev_sequence
124 if ( env_from - prev_env_to ) <= min_linker
125 extract_domain( sequence,
126 prev_number.to_s + "+" + number.to_s,
139 close_pairs_counter += 2
142 extract_domain( sequence,
148 out_msa_distant_partners,
155 distant_pairs_counter += 1
158 extract_domain( sequence,
164 out_msa_distant_partners,
171 distant_pairs_counter += 1
175 end # sequence != prev_sequence else
177 prev_sequence = sequence
179 prev_env_from = env_from
181 #prev_i_e_value = i_e_value
187 end # def process_hmmscan_data
190 # raises ArgumentError, IOError, StandardError
191 def parse( domain_id,
201 add_domain_number_as_digit,
202 add_domain_number_as_letter,
208 Util.check_file_for_readability( hmmscan_output )
209 Util.check_file_for_readability( fasta_sequence_file )
210 Util.check_file_for_writability( outfile )
211 Util.check_file_for_writability( passed_seqs_outfile )
212 Util.check_file_for_writability( failed_seqs_outfile )
215 factory = MsaFactory.new()
216 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
218 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
219 error_msg = "could not find fasta sequences in " + fasta_sequence_file
220 raise IOError, error_msg
225 failed_seqs = Msa.new
226 passed_seqs = Msa.new
228 out_msa_distant_partners = nil
229 out_msa_singles = nil
231 out_msa_pairs = Msa.new
232 out_msa_distant_partners = Msa.new
233 out_msa_singles = Msa.new
236 ld = Constants::LINE_DELIMITER
238 domain_pass_counter = 0
239 domain_fail_counter = 0
241 distant_pairs_counter = 0
242 close_pairs_counter = 0
243 proteins_with_failing_domains = 0
244 max_domain_copy_number_per_protein = -1
245 max_domain_copy_number_sequence = ""
251 # prev_i_e_value = nil
255 hmmscan_datas = Array.new
258 File.open( hmmscan_output ) do | file |
259 while line = file.gets
260 if !is_ignorable?( line ) && line =~ /^\S+\s+/
262 # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
263 # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
264 line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/
277 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
278 ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
279 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
280 if ( number > max_domain_copy_number_per_protein )
281 max_domain_copy_number_sequence = sequence
282 max_domain_copy_number_per_protein = number
285 print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
286 log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
287 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
288 print( " iE=" + i_e_value.to_s )
289 log << " iE=" + i_e_value.to_s
291 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
292 le = env_to - env_from + 1
293 print( " l=" + le.to_s )
294 log << " l=" + le.to_s
298 domain_fail_counter += 1
300 if failed_seqs.find_by_name_start( sequence, true ).length < 1
301 add_sequence( sequence, in_msa, failed_seqs )
302 proteins_with_failing_domains += 1
307 error_msg = "number > out_of ! (this should not have happened)"
308 raise StandardError, error_msg
311 if number == out_of && !hmmscan_datas.empty?
312 domain_pass_counter += process_hmmscan_datas( hmmscan_datas,
326 end # while line = file.gets
327 end # File.open( hmmsearch_output ) do | file |
331 if domain_pass_counter < 1
332 error_msg = "no domain sequences were extracted"
333 raise IOError, error_msg
337 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
338 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
341 if ( max_domain_copy_number_per_protein > 1 )
342 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
343 log << "First protein with this copy number: " + max_domain_copy_number_sequence
347 write_msa( out_msa, outfile )
348 write_msa( passed_seqs, passed_seqs_outfile )
349 write_msa( failed_seqs, failed_seqs_outfile )
352 write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s )
356 write_msa( out_msa_singles, outfile +"_singles" )
359 if out_msa_distant_partners
360 write_msa( out_msa_distant_partners, outfile + "_" + min_linker.to_s + "_isolated" );
365 log << "passing domains : " + domain_pass_counter.to_s + ld
367 log << "single domains : " + singlets_counter.to_s + ld
368 log << "domains in close pairs : " + close_pairs_counter.to_s + ld
369 log << "isolated domains : " + distant_pairs_counter.to_s + ld
371 log << "failing domains : " + domain_fail_counter.to_s + ld
372 log << "proteins with passing domains: " + passed_seqs.length.to_s + ld
373 log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
376 return domain_pass_counter
383 def write_msa( msa, filename )
385 w = FastaWriter.new()
386 w.set_line_width( 60 )
389 io.write_to_file( msa, filename, w )
391 error_msg = "could not write to \"" + filename + "\""
392 raise IOError, error_msg
397 def add_sequence( sequence_name, in_msa, add_to_msa )
398 seqs = in_msa.find_by_name_start( sequence_name, true )
399 if ( seqs.length < 1 )
400 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
401 raise StandardError, error_msg
403 if ( seqs.length > 1 )
404 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
405 raise StandardError, error_msg
407 seq = in_msa.get_sequence( seqs[ 0 ] )
408 add_to_msa.add_sequence( seq )
412 def extract_domain( sequence,
423 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
424 error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
425 raise StandardError, error_msg
427 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
428 error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
429 raise StandardError, error_msg
431 seqs = in_msa.find_by_name_start( sequence, true )
433 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
434 raise IOError, error_msg
437 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
438 raise IOError, error_msg
440 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
441 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
443 orig_name = seq.get_name
445 seq.set_name( orig_name.split[ 0 ] )
448 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
452 seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] )
455 if out_of != 1 && add_domain_number
456 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
460 a = orig_name.rindex "["
461 b = orig_name.rindex "]"
463 error_msg = "species not found in " + orig_name
464 raise StandardError, error_msg
466 species = orig_name[ a .. b ]
467 seq.set_name( seq.get_name + " " + species )
469 out_msa.add_sequence( seq )
472 def is_ignorable?( line )
473 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
476 end # class HmmscanDomainExtractor
479 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
485 @i_e_value = i_e_value
487 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value