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'
15 require 'lib/evo/io/parser/hmmscan_parser'
21 class HmmscanDomainExtractor
26 # raises ArgumentError, IOError, StandardError
41 Util.check_file_for_readability( hmmscan_output )
42 Util.check_file_for_readability( fasta_sequence_file )
43 Util.check_file_for_writability( outfile + ".fasta" )
44 Util.check_file_for_writability( passed_seqs_outfile )
45 Util.check_file_for_writability( failed_seqs_outfile )
48 factory = MsaFactory.new()
49 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
51 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
52 error_msg = "could not find fasta sequences in " + fasta_sequence_file
53 raise IOError, error_msg
61 out_msa_isolated = nil
63 out_msa_single_domains_protein_seqs = nil
64 out_msa_close_pairs_protein_seqs = nil
65 out_msa_close_pairs_only_protein_seqs = nil
66 out_msa_isolated_protein_seqs = nil
67 out_msa_isolated_only_protein_seqs = nil
68 out_msa_isolated_and_close_pair_protein_seqs = nil
70 out_msa_pairs = Msa.new
71 out_msa_isolated = Msa.new
72 out_msa_singles = Msa.new
73 out_msa_single_domains_protein_seqs = Msa.new
74 out_msa_close_pairs_protein_seqs = Msa.new
75 out_msa_close_pairs_only_protein_seqs = Msa.new
76 out_msa_isolated_protein_seqs = Msa.new
77 out_msa_isolated_only_protein_seqs = Msa.new
78 out_msa_isolated_and_close_pair_protein_seqs = Msa.new
81 ld = Constants::LINE_DELIMITER
83 domain_pass_counter = 0
84 domain_fail_counter = 0
85 proteins_with_failing_domains = 0
86 max_domain_copy_number_per_protein = -1
87 max_domain_copy_number_sequence = ""
91 hmmscan_parser = HmmscanParser.new( hmmscan_output )
92 results = hmmscan_parser.parse
95 if domain_id != r.model
102 env_from = r.env_from
104 i_e_value = r.i_e_value
106 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
107 ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
108 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
109 if ( number > max_domain_copy_number_per_protein )
110 max_domain_copy_number_sequence = sequence
111 max_domain_copy_number_per_protein = number
114 print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
115 log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
116 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
117 print( " iE=" + i_e_value.to_s )
118 log << " iE=" + i_e_value.to_s
120 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
121 le = env_to - env_from + 1
122 print( " l=" + le.to_s )
123 log << " l=" + le.to_s
127 domain_fail_counter += 1
131 error_msg = "number > out_of ! (this should not have happened)"
132 raise StandardError, error_msg
136 if !hmmscan_datas.empty?
137 process_hmmscan_datas( hmmscan_datas,
147 out_msa_single_domains_protein_seqs,
148 out_msa_close_pairs_protein_seqs,
149 out_msa_close_pairs_only_protein_seqs,
150 out_msa_isolated_protein_seqs,
151 out_msa_isolated_only_protein_seqs,
152 out_msa_isolated_and_close_pair_protein_seqs )
153 domain_pass_counter += hmmscan_datas.length
154 if passed_seqs.find_by_name_start( sequence, true ).length < 1
155 add_sequence( sequence, in_msa, passed_seqs )
157 error_msg = "this should not have happened"
158 raise StandardError, error_msg
161 if failed_seqs.find_by_name_start( sequence, true ).length < 1
162 add_sequence( sequence, in_msa, failed_seqs )
163 proteins_with_failing_domains += 1
165 error_msg = "this should not have happened"
166 raise StandardError, error_msg
173 if domain_pass_counter < 1
174 error_msg = "no domain sequences were extracted"
175 raise IOError, error_msg
179 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
180 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
183 if ( max_domain_copy_number_per_protein > 1 )
184 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
185 log << "First protein with this copy number: " + max_domain_copy_number_sequence
189 write_msa( out_msa, outfile + ".fasta" )
190 write_msa( passed_seqs, passed_seqs_outfile )
191 write_msa( failed_seqs, failed_seqs_outfile )
194 write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
198 write_msa( out_msa_singles, outfile +"_singles.fasta")
202 write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
205 if out_msa_single_domains_protein_seqs
206 write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" )
209 if out_msa_close_pairs_protein_seqs
210 write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
213 if out_msa_close_pairs_only_protein_seqs
214 write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
217 if out_msa_isolated_protein_seqs
218 write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
221 if out_msa_isolated_only_protein_seqs
222 write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
225 if out_msa_isolated_and_close_pair_protein_seqs
226 write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
230 if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
231 out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
232 out_msa_isolated_only_protein_seqs.get_number_of_seqs +
233 out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
234 error_msg = "this should not have happened"
235 raise StandardError, error_msg
240 log << "passing domains : " + domain_pass_counter.to_s + ld
241 log << "failing domains : " + domain_fail_counter.to_s + ld
242 log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld
243 log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld
244 log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld
246 log << "min linker length : " + min_linker.to_s + ld
247 log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
248 log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
249 log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
250 log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
251 log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
252 log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
253 log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
254 log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
255 log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
260 return domain_pass_counter
267 def write_msa( msa, filename )
269 w = FastaWriter.new()
270 w.set_line_width( 60 )
273 io.write_to_file( msa, filename, w )
275 error_msg = "could not write to \"" + filename + "\""
276 raise IOError, error_msg
281 def add_sequence( sequence_name, in_msa, add_to_msa )
282 seqs = in_msa.find_by_name_start( sequence_name, true )
283 if ( seqs.length < 1 )
284 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
285 raise StandardError, error_msg
287 if ( seqs.length > 1 )
288 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
289 raise StandardError, error_msg
291 seq = in_msa.get_sequence( seqs[ 0 ] )
292 add_to_msa.add_sequence( seq )
295 def process_hmmscan_datas( hmmscan_datas,
305 out_msa_single_domains_protein_seqs,
306 out_msa_close_pairs_protein_seqs,
307 out_msa_close_pairs_only_protein_seqs,
308 out_msa_isolated_protein_seqs,
309 out_msa_isolated_only_protein_seqs,
310 out_msa_isolated_and_close_pair_protein_seqs )
312 actual_out_of = hmmscan_datas.size
313 saw_close_pair = false
319 hmmscan_datas.each_with_index do |hmmscan_data, index|
320 if hmmscan_data.number < ( index + 1 )
321 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
322 raise StandardError, error_msg
325 seq_name = hmmscan_data.seq_name
327 extract_domain( seq_name,
330 hmmscan_data.env_from,
339 if actual_out_of == 1
340 extract_domain( seq_name,
343 hmmscan_data.env_from,
350 if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
351 add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
353 error_msg = "this should not have happened"
354 raise StandardError, error_msg
359 last = index == hmmscan_datas.length - 1
361 if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
362 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
363 ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
364 ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
366 extract_domain( seq_name,
369 hmmscan_data.env_from,
379 extract_domain( seq_name,
380 index.to_s + "+" + ( index + 1 ).to_s,
382 hmmscan_datas[ index - 1 ].env_from,
389 saw_close_pair = true
393 if prev_seq_name && prev_seq_name != seq_name
394 error_msg = "this should not have happened"
395 raise StandardError, error_msg
397 prev_seq_name = seq_name
400 if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
401 add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
403 error_msg = "this should not have happened"
404 raise StandardError, error_msg
408 if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
409 add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
411 error_msg = "this should not have happened"
412 raise StandardError, error_msg
415 if saw_close_pair && saw_isolated
416 if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
417 add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
419 error_msg = "this should not have happened"
420 raise StandardError, error_msg
423 if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
424 add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
426 error_msg = "this should not have happened"
427 raise StandardError, error_msg
430 if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
431 add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
433 error_msg = "this should not have happened"
434 raise StandardError, error_msg
437 end # def process_hmmscan_data
439 def extract_domain( sequence,
449 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
450 error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
451 raise StandardError, error_msg
453 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
454 error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
455 raise StandardError, error_msg
457 seqs = in_msa.find_by_name_start( sequence, true )
459 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
460 raise IOError, error_msg
463 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
464 raise IOError, error_msg
466 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
467 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
469 orig_name = seq.get_name
471 seq.set_name( orig_name.split[ 0 ] )
474 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
477 if out_of != 1 && add_domain_number
478 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
482 a = orig_name.rindex "["
483 b = orig_name.rindex "]"
485 error_msg = "species not found in " + orig_name
486 raise StandardError, error_msg
488 species = orig_name[ a .. b ]
489 seq.set_name( seq.get_name + " " + species )
491 out_msa.add_sequence( seq )
494 def is_ignorable?( line )
495 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
498 end # class HmmscanDomainExtractor
501 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
507 @i_e_value = i_e_value
509 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value