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
24 # raises ArgumentError, IOError, StandardError
39 Util.check_file_for_readability( hmmscan_output )
40 Util.check_file_for_readability( fasta_sequence_file )
41 Util.check_file_for_writability( outfile + ".fasta" )
42 Util.check_file_for_writability( passed_seqs_outfile )
43 Util.check_file_for_writability( failed_seqs_outfile )
46 factory = MsaFactory.new()
47 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
49 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
50 error_msg = "could not find fasta sequences in " + fasta_sequence_file
51 raise IOError, error_msg
59 out_msa_isolated = nil
61 out_msa_single_domains_protein_seqs = nil
62 out_msa_close_pairs_protein_seqs = nil
63 out_msa_close_pairs_only_protein_seqs = nil
64 out_msa_isolated_protein_seqs = nil
65 out_msa_isolated_only_protein_seqs = nil
66 out_msa_isolated_and_close_pair_protein_seqs = nil
68 out_msa_pairs = Msa.new
69 out_msa_isolated = Msa.new
70 out_msa_singles = Msa.new
71 out_msa_single_domains_protein_seqs = Msa.new
72 out_msa_close_pairs_protein_seqs = Msa.new
73 out_msa_close_pairs_only_protein_seqs = Msa.new
74 out_msa_isolated_protein_seqs = Msa.new
75 out_msa_isolated_only_protein_seqs = Msa.new
76 out_msa_isolated_and_close_pair_protein_seqs = Msa.new
79 ld = Constants::LINE_DELIMITER
81 domain_pass_counter = 0
82 domain_fail_counter = 0
83 proteins_with_failing_domains = 0
84 max_domain_copy_number_per_protein = -1
85 max_domain_copy_number_sequence = ""
87 hmmscan_datas = Array.new
89 File.open( hmmscan_output ) do | file |
90 while line = file.gets
91 if !is_ignorable?( line ) && line =~ /^\S+\s+/
93 # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
94 # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
95 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+(.*)/
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 end # while line = file.gets
176 end # File.open( hmmsearch_output ) do | file |
178 if domain_pass_counter < 1
179 error_msg = "no domain sequences were extracted"
180 raise IOError, error_msg
184 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
185 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
188 if ( max_domain_copy_number_per_protein > 1 )
189 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
190 log << "First protein with this copy number: " + max_domain_copy_number_sequence
194 write_msa( out_msa, outfile + ".fasta" )
195 write_msa( passed_seqs, passed_seqs_outfile )
196 write_msa( failed_seqs, failed_seqs_outfile )
199 write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
203 write_msa( out_msa_singles, outfile +"_singles.fasta")
207 write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
210 if out_msa_single_domains_protein_seqs
211 write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" )
214 if out_msa_close_pairs_protein_seqs
215 write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
218 if out_msa_close_pairs_only_protein_seqs
219 write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
222 if out_msa_isolated_protein_seqs
223 write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
226 if out_msa_isolated_only_protein_seqs
227 write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
230 if out_msa_isolated_and_close_pair_protein_seqs
231 write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
235 if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
236 out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
237 out_msa_isolated_only_protein_seqs.get_number_of_seqs +
238 out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
239 error_msg = "this should not have happened"
240 raise StandardError, error_msg
245 log << "passing domains : " + domain_pass_counter.to_s + ld
246 log << "failing domains : " + domain_fail_counter.to_s + ld
247 log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld
248 log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld
249 log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld
251 log << "min linker length : " + min_linker.to_s + ld
252 log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
253 log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
254 log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
255 log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
256 log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
257 log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
258 log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
259 log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
260 log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
265 return domain_pass_counter
272 def write_msa( msa, filename )
274 w = FastaWriter.new()
275 w.set_line_width( 60 )
278 io.write_to_file( msa, filename, w )
280 error_msg = "could not write to \"" + filename + "\""
281 raise IOError, error_msg
286 def add_sequence( sequence_name, in_msa, add_to_msa )
287 seqs = in_msa.find_by_name_start( sequence_name, true )
288 if ( seqs.length < 1 )
289 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
290 raise StandardError, error_msg
292 if ( seqs.length > 1 )
293 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
294 raise StandardError, error_msg
296 seq = in_msa.get_sequence( seqs[ 0 ] )
297 add_to_msa.add_sequence( seq )
300 def process_hmmscan_datas( hmmscan_datas,
310 out_msa_single_domains_protein_seqs,
311 out_msa_close_pairs_protein_seqs,
312 out_msa_close_pairs_only_protein_seqs,
313 out_msa_isolated_protein_seqs,
314 out_msa_isolated_only_protein_seqs,
315 out_msa_isolated_and_close_pair_protein_seqs )
317 actual_out_of = hmmscan_datas.size
318 saw_close_pair = false
324 hmmscan_datas.each_with_index do |hmmscan_data, index|
325 if hmmscan_data.number < ( index + 1 )
326 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
327 raise StandardError, error_msg
330 seq_name = hmmscan_data.seq_name
332 extract_domain( seq_name,
335 hmmscan_data.env_from,
344 if actual_out_of == 1
345 extract_domain( seq_name,
348 hmmscan_data.env_from,
355 if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
356 add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
358 error_msg = "this should not have happened"
359 raise StandardError, error_msg
364 last = index == hmmscan_datas.length - 1
366 if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
367 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
368 ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
369 ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
371 extract_domain( seq_name,
374 hmmscan_data.env_from,
384 extract_domain( seq_name,
385 index.to_s + "+" + ( index + 1 ).to_s,
387 hmmscan_datas[ index - 1 ].env_from,
394 saw_close_pair = true
398 if prev_seq_name && prev_seq_name != seq_name
399 error_msg = "this should not have happened"
400 raise StandardError, error_msg
402 prev_seq_name = seq_name
405 if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
406 add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
408 error_msg = "this should not have happened"
409 raise StandardError, error_msg
413 if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
414 add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
416 error_msg = "this should not have happened"
417 raise StandardError, error_msg
420 if saw_close_pair && saw_isolated
421 if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
422 add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
424 error_msg = "this should not have happened"
425 raise StandardError, error_msg
428 if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
429 add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
431 error_msg = "this should not have happened"
432 raise StandardError, error_msg
435 if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
436 add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
438 error_msg = "this should not have happened"
439 raise StandardError, error_msg
442 end # def process_hmmscan_data
444 def extract_domain( sequence,
454 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
455 error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
456 raise StandardError, error_msg
458 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
459 error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
460 raise StandardError, error_msg
462 seqs = in_msa.find_by_name_start( sequence, true )
464 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
465 raise IOError, error_msg
468 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
469 raise IOError, error_msg
471 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
472 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
474 orig_name = seq.get_name
476 seq.set_name( orig_name.split[ 0 ] )
479 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
482 if out_of != 1 && add_domain_number
483 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
487 a = orig_name.rindex "["
488 b = orig_name.rindex "]"
490 error_msg = "species not found in " + orig_name
491 raise StandardError, error_msg
493 species = orig_name[ a .. b ]
494 seq.set_name( seq.get_name + " " + species )
496 out_msa.add_sequence( seq )
499 def is_ignorable?( line )
500 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
503 end # class HmmscanDomainExtractor
506 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
512 @i_e_value = i_e_value
514 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value