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
23 ADD_TO_CLOSE_PAIRS = 0
28 # raises ArgumentError, IOError, StandardError
43 Util.check_file_for_readability( hmmscan_output )
44 Util.check_file_for_readability( fasta_sequence_file )
45 Util.check_file_for_writability( outfile + ".fasta" )
46 Util.check_file_for_writability( passed_seqs_outfile )
47 Util.check_file_for_writability( failed_seqs_outfile )
50 factory = MsaFactory.new()
51 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
53 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
54 error_msg = "could not find fasta sequences in " + fasta_sequence_file
55 raise IOError, error_msg
63 out_msa_isolated = nil
65 out_msa_single_domains_protein_seqs = nil
66 out_msa_close_pairs_protein_seqs = nil
67 out_msa_close_pairs_only_protein_seqs = nil
68 out_msa_isolated_protein_seqs = nil
69 out_msa_isolated_only_protein_seqs = nil
70 out_msa_isolated_and_close_pair_protein_seqs = nil
72 out_msa_pairs = Msa.new
73 out_msa_isolated = Msa.new
74 out_msa_singles = Msa.new
75 out_msa_single_domains_protein_seqs = Msa.new
76 out_msa_close_pairs_protein_seqs = Msa.new
77 out_msa_close_pairs_only_protein_seqs = Msa.new
78 out_msa_isolated_protein_seqs = Msa.new
79 out_msa_isolated_only_protein_seqs = Msa.new
80 out_msa_isolated_and_close_pair_protein_seqs = Msa.new
83 ld = Constants::LINE_DELIMITER
85 domain_pass_counter = 0
86 domain_fail_counter = 0
87 proteins_with_failing_domains = 0
88 max_domain_copy_number_per_protein = -1
89 max_domain_copy_number_sequence = ""
93 hmmscan_parser = HmmscanParser.new( hmmscan_output )
94 results = hmmscan_parser.parse
97 if domain_id != r.model
104 env_from = r.env_from
106 i_e_value = r.i_e_value
108 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
109 ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
110 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
111 if ( number > max_domain_copy_number_per_protein )
112 max_domain_copy_number_sequence = sequence
113 max_domain_copy_number_per_protein = number
116 print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
117 log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
118 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
119 print( " iE=" + i_e_value.to_s )
120 log << " iE=" + i_e_value.to_s
122 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
123 le = env_to - env_from + 1
124 print( " l=" + le.to_s )
125 log << " l=" + le.to_s
129 domain_fail_counter += 1
133 error_msg = "number > out_of ! (this should not have happened)"
134 raise StandardError, error_msg
138 if !hmmscan_datas.empty?
139 process_hmmscan_datas( hmmscan_datas,
149 out_msa_single_domains_protein_seqs,
150 out_msa_close_pairs_protein_seqs,
151 out_msa_close_pairs_only_protein_seqs,
152 out_msa_isolated_protein_seqs,
153 out_msa_isolated_only_protein_seqs,
154 out_msa_isolated_and_close_pair_protein_seqs )
155 domain_pass_counter += hmmscan_datas.length
156 if passed_seqs.find_by_name_start( sequence, true ).length < 1
157 add_sequence( sequence, in_msa, passed_seqs )
159 error_msg = "this should not have happened"
160 raise StandardError, error_msg
163 if failed_seqs.find_by_name_start( sequence, true ).length < 1
164 add_sequence( sequence, in_msa, failed_seqs )
165 proteins_with_failing_domains += 1
167 error_msg = "this should not have happened"
168 raise StandardError, error_msg
175 if domain_pass_counter < 1
176 error_msg = "no domain sequences were extracted"
177 raise IOError, error_msg
181 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
182 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
185 if ( max_domain_copy_number_per_protein > 1 )
186 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
187 log << "First protein with this copy number: " + max_domain_copy_number_sequence
191 write_msa( out_msa, outfile + ".fasta" )
192 write_msa( passed_seqs, passed_seqs_outfile )
193 write_msa( failed_seqs, failed_seqs_outfile )
196 write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
200 write_msa( out_msa_singles, outfile +"_singles.fasta")
204 write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
207 if out_msa_single_domains_protein_seqs
208 write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" )
211 if out_msa_close_pairs_protein_seqs
212 write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
215 if out_msa_close_pairs_only_protein_seqs
216 write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
219 if out_msa_isolated_protein_seqs
220 write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
223 if out_msa_isolated_only_protein_seqs
224 write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
227 if out_msa_isolated_and_close_pair_protein_seqs
228 write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
232 if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
233 out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
234 out_msa_isolated_only_protein_seqs.get_number_of_seqs +
235 out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
236 error_msg = "this should not have happened"
237 raise StandardError, error_msg
242 log << "passing domains : " + domain_pass_counter.to_s + ld
243 log << "failing domains : " + domain_fail_counter.to_s + ld
244 log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld
245 log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld
246 log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld
248 log << "min linker length : " + min_linker.to_s + ld
249 log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
250 log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
251 log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
252 log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
253 log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
254 log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
255 log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
256 log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
257 log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
262 return domain_pass_counter
269 def write_msa( msa, filename )
271 w = FastaWriter.new()
272 w.set_line_width( 60 )
275 io.write_to_file( msa, filename, w )
277 error_msg = "could not write to \"" + filename + "\""
278 raise IOError, error_msg
283 def add_sequence( sequence_name, in_msa, add_to_msa )
284 seqs = in_msa.find_by_name_start( sequence_name, true )
285 if ( seqs.length < 1 )
286 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
287 raise StandardError, error_msg
289 if ( seqs.length > 1 )
290 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
291 raise StandardError, error_msg
293 seq = in_msa.get_sequence( seqs[ 0 ] )
294 add_to_msa.add_sequence( seq )
297 def process_hmmscan_datas( hmmscan_datas,
307 out_msa_single_domains_protein_seqs,
308 out_msa_close_pairs_protein_seqs,
309 out_msa_close_pairs_only_protein_seqs,
310 out_msa_isolated_protein_seqs,
311 out_msa_isolated_only_protein_seqs,
312 out_msa_isolated_and_close_pair_protein_seqs )
314 actual_out_of = hmmscan_datas.size
315 saw_close_pair = false
321 hmmscan_datas.each_with_index do |hmmscan_data, index|
322 if hmmscan_data.number < ( index + 1 )
323 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
324 raise StandardError, error_msg
327 seq_name = hmmscan_data.seq_name
329 extract_domain( seq_name,
332 hmmscan_data.env_from,
341 if actual_out_of == 1
342 extract_domain( seq_name,
345 hmmscan_data.env_from,
352 if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
353 add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
355 error_msg = "this should not have happened"
356 raise StandardError, error_msg
361 last = index == hmmscan_datas.length - 1
363 if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
364 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
365 ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
366 ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
368 extract_domain( seq_name,
371 hmmscan_data.env_from,
382 from = hmmscan_datas[ index - 1 ].env_from
383 to = hmmscan_data.env_to
385 if ADD_TO_CLOSE_PAIRS > 0
386 from = from - ADD_TO_CLOSE_PAIRS
390 to = to + ADD_TO_CLOSE_PAIRS
391 temp_seqs = in_msa.find_by_name_start( seq_name, true )
392 temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] )
393 if to > temp_seq.get_length
394 to = temp_seq.get_length
398 extract_domain( seq_name,
399 index.to_s + "+" + ( index + 1 ).to_s,
408 saw_close_pair = true
412 if prev_seq_name && prev_seq_name != seq_name
413 error_msg = "this should not have happened"
414 raise StandardError, error_msg
416 prev_seq_name = seq_name
419 if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
420 add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
422 error_msg = "this should not have happened"
423 raise StandardError, error_msg
427 if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
428 add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
430 error_msg = "this should not have happened"
431 raise StandardError, error_msg
434 if saw_close_pair && saw_isolated
435 if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
436 add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
438 error_msg = "this should not have happened"
439 raise StandardError, error_msg
442 if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
443 add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
445 error_msg = "this should not have happened"
446 raise StandardError, error_msg
449 if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
450 add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
452 error_msg = "this should not have happened"
453 raise StandardError, error_msg
456 end # def process_hmmscan_data
458 def extract_domain( sequence,
468 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
469 error_msg = "number=" + number.to_s + ", out of=" + out_of.to_s
470 raise StandardError, error_msg
472 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
473 error_msg = "impossible: seq-from=" + seq_from.to_s + ", seq-to=" + seq_to.to_s
474 raise StandardError, error_msg
476 seqs = in_msa.find_by_name_start( sequence, true )
478 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
479 raise IOError, error_msg
482 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
483 raise IOError, error_msg
485 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
486 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
488 orig_name = seq.get_name
490 seq.set_name( orig_name.split[ 0 ] )
493 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
496 if out_of != 1 && add_domain_number
497 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
501 a = orig_name.rindex "["
502 b = orig_name.rindex "]"
504 error_msg = "species not found in " + orig_name
505 raise StandardError, error_msg
507 species = orig_name[ a .. b ]
508 seq.set_name( seq.get_name + " " + species )
510 out_msa.add_sequence( seq )
513 def is_ignorable?( line )
514 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
517 end # class HmmscanDomainExtractor
520 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
526 @i_e_value = i_e_value
528 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value