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 require 'lib/evo/util/constants'
8 require 'lib/evo/msa/msa_factory'
9 require 'lib/evo/io/msa_io'
10 require 'lib/evo/io/writer/fasta_writer'
11 require 'lib/evo/io/parser/fasta_parser'
12 require 'lib/evo/io/parser/hmmscan_parser'
15 class HmmscanDomainExtractor
17 ADD_TO_CLOSE_PAIRS = 0
21 # raises ArgumentError, IOError, StandardError
36 Util.check_file_for_readability( hmmscan_output )
37 Util.check_file_for_readability( fasta_sequence_file )
38 Util.check_file_for_writability( outfile + ".fasta" )
39 Util.check_file_for_writability( passed_seqs_outfile )
40 Util.check_file_for_writability( failed_seqs_outfile )
43 factory = MsaFactory.new()
44 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
46 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
47 error_msg = "could not find fasta sequences in " + fasta_sequence_file
48 raise IOError, error_msg
56 out_msa_isolated = nil
58 out_msa_single_domains_protein_seqs = nil
59 out_msa_close_pairs_protein_seqs = nil
60 out_msa_close_pairs_only_protein_seqs = nil
61 out_msa_isolated_protein_seqs = nil
62 out_msa_isolated_only_protein_seqs = nil
63 out_msa_isolated_and_close_pair_protein_seqs = nil
65 out_msa_pairs = Msa.new
66 out_msa_isolated = Msa.new
67 out_msa_singles = Msa.new
68 out_msa_single_domains_protein_seqs = Msa.new
69 out_msa_close_pairs_protein_seqs = Msa.new
70 out_msa_close_pairs_only_protein_seqs = Msa.new
71 out_msa_isolated_protein_seqs = Msa.new
72 out_msa_isolated_only_protein_seqs = Msa.new
73 out_msa_isolated_and_close_pair_protein_seqs = Msa.new
76 ld = Constants::LINE_DELIMITER
78 domain_pass_counter = 0
79 domain_fail_counter = 0
80 proteins_with_failing_domains = 0
81 max_domain_copy_number_per_protein = -1
82 max_domain_copy_number_sequence = ""
86 hmmscan_parser = HmmscanParser.new( hmmscan_output )
87 results = hmmscan_parser.parse
90 if domain_id != r.model
99 i_e_value = r.i_e_value
101 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
102 ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
103 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
104 if ( number > max_domain_copy_number_per_protein )
105 max_domain_copy_number_sequence = sequence
106 max_domain_copy_number_per_protein = number
109 print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
110 log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
111 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
112 print( " iE=" + i_e_value.to_s )
113 log << " iE=" + i_e_value.to_s
115 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
116 le = env_to - env_from + 1
117 print( " l=" + le.to_s )
118 log << " l=" + le.to_s
122 domain_fail_counter += 1
126 error_msg = "number > out_of ! (this should not have happened)"
127 raise StandardError, error_msg
131 if !hmmscan_datas.empty?
132 process_hmmscan_datas( hmmscan_datas,
142 out_msa_single_domains_protein_seqs,
143 out_msa_close_pairs_protein_seqs,
144 out_msa_close_pairs_only_protein_seqs,
145 out_msa_isolated_protein_seqs,
146 out_msa_isolated_only_protein_seqs,
147 out_msa_isolated_and_close_pair_protein_seqs )
148 domain_pass_counter += hmmscan_datas.length
149 if passed_seqs.find_by_name_start( sequence, true ).length < 1
150 add_sequence( sequence, in_msa, passed_seqs )
152 error_msg = "this should not have happened"
153 raise StandardError, error_msg
156 if failed_seqs.find_by_name_start( sequence, true ).length < 1
157 add_sequence( sequence, in_msa, failed_seqs )
158 proteins_with_failing_domains += 1
160 error_msg = "this should not have happened"
161 raise StandardError, error_msg
168 if domain_pass_counter < 1
169 error_msg = "no domain sequences were extracted"
170 raise IOError, error_msg
174 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
175 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
178 if ( max_domain_copy_number_per_protein > 1 )
179 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
180 log << "First protein with this copy number: " + max_domain_copy_number_sequence
184 write_msa( out_msa, outfile + ".fasta" )
185 write_msa( passed_seqs, passed_seqs_outfile )
186 write_msa( failed_seqs, failed_seqs_outfile )
189 write_msa( out_msa_pairs, outfile + "_" + min_linker.to_s + ".fasta")
193 write_msa( out_msa_singles, outfile + "_singles.fasta")
197 write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
200 if out_msa_single_domains_protein_seqs
201 write_msa( out_msa_single_domains_protein_seqs, outfile + "_proteins_with_singles.fasta" )
204 if out_msa_close_pairs_protein_seqs
205 write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
208 if out_msa_close_pairs_only_protein_seqs
209 write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
212 if out_msa_isolated_protein_seqs
213 write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
216 if out_msa_isolated_only_protein_seqs
217 write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
220 if out_msa_isolated_and_close_pair_protein_seqs
221 write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
225 if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
226 out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
227 out_msa_isolated_only_protein_seqs.get_number_of_seqs +
228 out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
229 error_msg = "this should not have happened"
230 raise StandardError, error_msg
235 log << "passing domains : " + domain_pass_counter.to_s + ld
236 log << "failing domains : " + domain_fail_counter.to_s + ld
237 log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld
238 log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld
239 log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld
241 log << "min linker length : " + min_linker.to_s + ld
242 log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
243 log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
244 log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
245 log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
246 log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
247 log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
248 log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
249 log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
250 log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
255 return domain_pass_counter
261 def write_msa( msa, filename )
263 w = FastaWriter.new()
264 w.set_line_width( 60 )
267 io.write_to_file( msa, filename, w )
269 error_msg = "could not write to \"" + filename + "\""
270 raise IOError, error_msg
274 def add_sequence( sequence_name, in_msa, add_to_msa )
275 seqs = in_msa.find_by_name_start( sequence_name, true )
276 if ( seqs.length < 1 )
277 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
278 raise StandardError, error_msg
280 if ( seqs.length > 1 )
281 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
282 raise StandardError, error_msg
284 seq = in_msa.get_sequence( seqs[ 0 ] )
285 add_to_msa.add_sequence( seq )
288 def process_hmmscan_datas( hmmscan_datas,
298 out_msa_single_domains_protein_seqs,
299 out_msa_close_pairs_protein_seqs,
300 out_msa_close_pairs_only_protein_seqs,
301 out_msa_isolated_protein_seqs,
302 out_msa_isolated_only_protein_seqs,
303 out_msa_isolated_and_close_pair_protein_seqs )
305 actual_out_of = hmmscan_datas.size
306 saw_close_pair = false
312 hmmscan_datas.each_with_index do |hmmscan_data, index|
313 if hmmscan_data.number < ( index + 1 )
314 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
315 raise StandardError, error_msg
318 seq_name = hmmscan_data.seq_name
320 extract_domain( seq_name,
323 hmmscan_data.env_from,
332 if actual_out_of == 1
333 extract_domain( seq_name,
336 hmmscan_data.env_from,
343 if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
344 add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
346 error_msg = "this should not have happened"
347 raise StandardError, error_msg
352 last = index == hmmscan_datas.length - 1
354 if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
355 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
356 ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
357 ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
359 extract_domain( seq_name,
362 hmmscan_data.env_from,
373 from = hmmscan_datas[ index - 1 ].env_from
374 to = hmmscan_data.env_to
376 if ADD_TO_CLOSE_PAIRS > 0
377 from = from - ADD_TO_CLOSE_PAIRS
381 to = to + ADD_TO_CLOSE_PAIRS
382 temp_seqs = in_msa.find_by_name_start( seq_name, true )
383 temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] )
384 if to > temp_seq.get_length
385 to = temp_seq.get_length
389 extract_domain( seq_name,
390 index.to_s + "+" + ( index + 1 ).to_s,
399 saw_close_pair = true
403 if prev_seq_name && prev_seq_name != seq_name
404 error_msg = "this should not have happened"
405 raise StandardError, error_msg
407 prev_seq_name = seq_name
410 if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
411 add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
413 error_msg = "this should not have happened"
414 raise StandardError, error_msg
418 if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
419 add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
421 error_msg = "this should not have happened"
422 raise StandardError, error_msg
425 if saw_close_pair && saw_isolated
426 if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
427 add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
429 error_msg = "this should not have happened"
430 raise StandardError, error_msg
433 if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
434 add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
436 error_msg = "this should not have happened"
437 raise StandardError, error_msg
440 if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
441 add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
443 error_msg = "this should not have happened"
444 raise StandardError, error_msg
447 end # def process_hmmscan_data
449 def extract_domain( sequence,
459 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
460 error_msg = "number=" + number.to_s + ", out of=" + out_of.to_s
461 raise StandardError, error_msg
463 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
464 error_msg = "impossible: seq-from=" + seq_from.to_s + ", seq-to=" + seq_to.to_s
465 raise StandardError, error_msg
467 seqs = in_msa.find_by_name_start( sequence, true )
469 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
470 raise IOError, error_msg
473 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
474 raise IOError, error_msg
476 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
477 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
479 orig_name = seq.get_name
481 seq.set_name( orig_name.split[ 0 ] )
484 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
487 if out_of != 1 && add_domain_number
488 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
492 a = orig_name.rindex "["
493 b = orig_name.rindex "]"
495 error_msg = "species not found in " + orig_name
496 raise StandardError, error_msg
498 species = orig_name[ a .. b ]
499 seq.set_name( seq.get_name + " " + species )
501 out_msa.add_sequence( seq )
504 def is_ignorable?( line )
505 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
508 end # class HmmscanDomainExtractor
511 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
517 @i_e_value = i_e_value
519 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value