2 # = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
4 # Copyright:: Copyright (C) 2017 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
7 # Last modified: 2017/02/16
9 require 'lib/evo/util/constants'
10 require 'lib/evo/msa/msa_factory'
11 require 'lib/evo/io/msa_io'
12 require 'lib/evo/io/writer/fasta_writer'
13 require 'lib/evo/io/parser/fasta_parser'
14 require 'lib/evo/io/parser/hmmscan_parser'
17 class HmmscanDomainExtractor
19 ADD_TO_CLOSE_PAIRS = 0
23 # raises ArgumentError, IOError, StandardError
38 Util.check_file_for_readability( hmmscan_output )
39 Util.check_file_for_readability( fasta_sequence_file )
40 Util.check_file_for_writability( outfile + ".fasta" )
41 Util.check_file_for_writability( passed_seqs_outfile )
42 Util.check_file_for_writability( failed_seqs_outfile )
45 factory = MsaFactory.new()
46 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
48 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
49 error_msg = "could not find fasta sequences in " + fasta_sequence_file
50 raise IOError, error_msg
58 out_msa_isolated = nil
60 out_msa_single_domains_protein_seqs = nil
61 out_msa_close_pairs_protein_seqs = nil
62 out_msa_close_pairs_only_protein_seqs = nil
63 out_msa_isolated_protein_seqs = nil
64 out_msa_isolated_only_protein_seqs = nil
65 out_msa_isolated_and_close_pair_protein_seqs = nil
67 out_msa_pairs = Msa.new
68 out_msa_isolated = Msa.new
69 out_msa_singles = Msa.new
70 out_msa_single_domains_protein_seqs = Msa.new
71 out_msa_close_pairs_protein_seqs = Msa.new
72 out_msa_close_pairs_only_protein_seqs = Msa.new
73 out_msa_isolated_protein_seqs = Msa.new
74 out_msa_isolated_only_protein_seqs = Msa.new
75 out_msa_isolated_and_close_pair_protein_seqs = Msa.new
78 ld = Constants::LINE_DELIMITER
80 domain_pass_counter = 0
81 domain_fail_counter = 0
82 proteins_with_failing_domains = 0
83 domain_not_present_counter = 0
85 max_domain_copy_number_per_protein = -1
86 max_domain_copy_number_sequence = ""
87 passing_target_length_sum = 0
88 overall_target_length_sum = 0
89 overall_target_length_min = 10000000
90 overall_target_length_max = 0
91 passing_target_length_min = 10000000
92 passing_target_length_max = 0
96 hmmscan_parser = HmmscanParser.new( hmmscan_output )
97 results = hmmscan_parser.parse
102 results.each do | r |
104 if ( prev_query != nil ) && ( r.query != prev_query )
107 log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld
108 domain_not_present_counter += 1
115 if domain_id != r.model
124 env_from = r.env_from
126 i_e_value = r.i_e_value
129 length = env_to - env_from + 1
131 overall_target_length_sum += length
132 if length > overall_target_length_max
133 overall_target_length_max = length
135 if length < overall_target_length_min
136 overall_target_length_min = length
139 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
140 ( ( length_threshold <= 0 ) || ( length >= length_threshold.to_f ) ) )
141 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
142 passing_target_length_sum += length
143 if length > passing_target_length_max
144 passing_target_length_max = length
146 if length < passing_target_length_min
147 passing_target_length_min = length
149 if ( number > max_domain_copy_number_per_protein )
150 max_domain_copy_number_sequence = sequence
151 max_domain_copy_number_per_protein = number
154 log << domain_fail_counter.to_s + ": " + sequence.to_s + " fails threshold(s)"
155 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
156 log << " iE=" + i_e_value.to_s
158 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
159 le = env_to - env_from + 1
160 log << " l=" + le.to_s
163 domain_fail_counter += 1
167 error_msg = "number > out_of (this should not have happened)"
168 raise StandardError, error_msg
172 if !hmmscan_datas.empty?
173 process_hmmscan_datas( hmmscan_datas,
183 out_msa_single_domains_protein_seqs,
184 out_msa_close_pairs_protein_seqs,
185 out_msa_close_pairs_only_protein_seqs,
186 out_msa_isolated_protein_seqs,
187 out_msa_isolated_only_protein_seqs,
188 out_msa_isolated_and_close_pair_protein_seqs )
189 domain_pass_counter += hmmscan_datas.length
190 if passed_seqs.find_by_name_start( sequence, true ).length < 1
191 add_sequence( sequence, in_msa, passed_seqs )
193 error_msg = "this should not have happened"
194 raise StandardError, error_msg
197 if failed_seqs.find_by_name_start( sequence, true ).length < 1
198 add_sequence( sequence, in_msa, failed_seqs )
199 proteins_with_failing_domains += 1
201 error_msg = "this should not have happened"
202 raise StandardError, error_msg
208 end # results.each do | r |
210 if (prev_query != nil) && (!saw_target)
211 log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld
212 domain_not_present_counter += 1
215 if domain_pass_counter < 1
216 error_msg = "no domain sequences were extracted"
217 raise IOError, error_msg
220 if ( domain_not_present_counter + passed_seqs.get_number_of_seqs + proteins_with_failing_domains ) != protein_counter
221 error_msg = "not present + passing + not passing != proteins in sequence (fasta) file (this should not have happened)"
222 raise StandardError, error_msg
229 avg_pass = ( passing_target_length_sum / domain_pass_counter )
230 puts( "Passing target domain lengths: average: " + avg_pass.to_s )
231 log << "Passing target domain lengths: average: " + avg_pass.to_s
233 puts( "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s)
234 log << "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s
236 puts( "Passing target domain lengths: sum: " + domain_pass_counter.to_s )
237 log << "Passing target domain lengths: sum: " + domain_pass_counter.to_s
241 sum = domain_pass_counter + domain_fail_counter
242 avg_all = overall_target_length_sum / sum
243 puts( "All target domain lengths: average: " + avg_all.to_s )
244 log << "All target domain lengths: average: " +avg_all.to_s
246 puts( "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s)
247 log << "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s
249 puts( "All target domain lengths: sum: " + sum.to_s )
250 log << "All target domain lengths: sum: " + sum.to_s
253 puts( "Proteins with passing target domain(s): " + passed_seqs.get_number_of_seqs.to_s )
254 puts( "Proteins with no passing target domain: " + proteins_with_failing_domains.to_s )
255 puts( "Proteins with no target domain : " + domain_not_present_counter.to_s )
260 puts( "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s )
261 log << "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s
264 if ( max_domain_copy_number_per_protein > 1 )
265 puts( "First target protein with this copy number: " + max_domain_copy_number_sequence )
266 log << "First target protein with this copy number: " + max_domain_copy_number_sequence
270 write_msa( out_msa, outfile + ".fasta" )
271 write_msa( passed_seqs, passed_seqs_outfile )
272 write_msa( failed_seqs, failed_seqs_outfile )
275 write_msa( out_msa_pairs, outfile + "_" + min_linker.to_s + ".fasta")
279 write_msa( out_msa_singles, outfile + "_singles.fasta")
283 write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
286 if out_msa_single_domains_protein_seqs
287 write_msa( out_msa_single_domains_protein_seqs, outfile + "_proteins_with_singles.fasta" )
290 if out_msa_close_pairs_protein_seqs
291 write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
294 if out_msa_close_pairs_only_protein_seqs
295 write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
298 if out_msa_isolated_protein_seqs
299 write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
302 if out_msa_isolated_only_protein_seqs
303 write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
306 if out_msa_isolated_and_close_pair_protein_seqs
307 write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
311 if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
312 out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
313 out_msa_isolated_only_protein_seqs.get_number_of_seqs +
314 out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
315 error_msg = "this should not have happened"
316 raise StandardError, error_msg
321 log << "passing target domains : " + domain_pass_counter.to_s + ld
322 log << "failing target domains : " + domain_fail_counter.to_s + ld
323 log << "proteins in sequence (fasta) file : " + in_msa.get_number_of_seqs.to_s + ld
324 log << "proteins in hmmscan outputfile : " + protein_counter.to_s + ld
325 log << "proteins with passing target domain(s) : " + passed_seqs.get_number_of_seqs.to_s + ld
326 log << "proteins with no passing target domain : " + proteins_with_failing_domains.to_s + ld
327 log << "proteins with no target domain : " + domain_not_present_counter.to_s + ld
329 log << "min linker length : " + min_linker.to_s + ld
330 log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
331 log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
332 log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
333 log << "proteins with single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
334 log << "proteins with close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
335 log << "proteins with close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
336 log << "proteins with isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
337 log << "proteins with isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
338 log << "proteins with close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
343 return domain_pass_counter
349 def write_msa( msa, filename )
351 w = FastaWriter.new()
352 w.set_line_width( 60 )
355 io.write_to_file( msa, filename, w )
357 error_msg = "could not write to \"" + filename + "\""
358 raise IOError, error_msg
362 def add_sequence( sequence_name, in_msa, add_to_msa )
363 seqs = in_msa.find_by_name_start( sequence_name, true )
364 if ( seqs.length < 1 )
365 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
366 raise StandardError, error_msg
368 if ( seqs.length > 1 )
369 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
370 raise StandardError, error_msg
372 seq = in_msa.get_sequence( seqs[ 0 ] )
373 add_to_msa.add_sequence( seq )
376 def process_hmmscan_datas( hmmscan_datas,
386 out_msa_single_domains_protein_seqs,
387 out_msa_close_pairs_protein_seqs,
388 out_msa_close_pairs_only_protein_seqs,
389 out_msa_isolated_protein_seqs,
390 out_msa_isolated_only_protein_seqs,
391 out_msa_isolated_and_close_pair_protein_seqs )
393 actual_out_of = hmmscan_datas.size
394 saw_close_pair = false
400 hmmscan_datas.each_with_index do |hmmscan_data, index|
401 if hmmscan_data.number < ( index + 1 )
402 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
403 raise StandardError, error_msg
406 seq_name = hmmscan_data.seq_name
408 extract_domain( seq_name,
411 hmmscan_data.env_from,
420 if actual_out_of == 1
421 extract_domain( seq_name,
424 hmmscan_data.env_from,
431 if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
432 add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
434 error_msg = "this should not have happened"
435 raise StandardError, error_msg
440 last = index == hmmscan_datas.length - 1
442 if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
443 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
444 ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
445 ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
447 extract_domain( seq_name,
450 hmmscan_data.env_from,
461 from = hmmscan_datas[ index - 1 ].env_from
462 to = hmmscan_data.env_to
464 if ADD_TO_CLOSE_PAIRS > 0
465 from = from - ADD_TO_CLOSE_PAIRS
469 to = to + ADD_TO_CLOSE_PAIRS
470 temp_seqs = in_msa.find_by_name_start( seq_name, true )
471 temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] )
472 if to > temp_seq.get_length
473 to = temp_seq.get_length
477 extract_domain( seq_name,
478 index.to_s + "+" + ( index + 1 ).to_s,
487 saw_close_pair = true
491 if prev_seq_name && prev_seq_name != seq_name
492 error_msg = "this should not have happened"
493 raise StandardError, error_msg
495 prev_seq_name = seq_name
498 if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
499 add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
501 error_msg = "this should not have happened"
502 raise StandardError, error_msg
506 if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
507 add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
509 error_msg = "this should not have happened"
510 raise StandardError, error_msg
513 if saw_close_pair && saw_isolated
514 if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
515 add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
517 error_msg = "this should not have happened"
518 raise StandardError, error_msg
521 if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
522 add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
524 error_msg = "this should not have happened"
525 raise StandardError, error_msg
528 if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
529 add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
531 error_msg = "this should not have happened"
532 raise StandardError, error_msg
535 end # def process_hmmscan_data
537 def extract_domain( sequence,
547 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
548 error_msg = "number=" + number.to_s + ", out of=" + out_of.to_s
549 raise StandardError, error_msg
551 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
552 error_msg = "impossible: seq-from=" + seq_from.to_s + ", seq-to=" + seq_to.to_s
553 raise StandardError, error_msg
555 seqs = in_msa.find_by_name_start( sequence, true )
557 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
558 raise IOError, error_msg
561 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
562 raise IOError, error_msg
564 # hmmscan is 1 based, whereas sequences are 0 bases in this package.
565 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
567 orig_name = seq.get_name
569 seq.set_name( orig_name.split[ 0 ] )
572 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
575 if out_of != 1 && add_domain_number
576 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
580 a = orig_name.rindex "["
581 b = orig_name.rindex "]"
583 error_msg = "species not found in " + orig_name
584 raise StandardError, error_msg
586 species = orig_name[ a .. b ]
587 seq.set_name( seq.get_name + " " + species )
589 out_msa.add_sequence( seq )
592 def is_ignorable?( line )
593 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
596 end # class HmmscanDomainExtractor
599 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
605 @i_e_value = i_e_value
607 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value