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
27 def process_hmmscan_datas( hmmscan_datas,
35 actual_out_of = hmmscan_datas.size
37 domain_pass_counter = 0;
39 hmmscan_datas.each_with_index do |hmmscan_data, index|
40 if hmmscan_data.number < ( index + 1 )
41 error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
42 raise StandardError, error_msg
45 extract_domain( hmmscan_data.seq_name,
48 hmmscan_data.env_from,
56 domain_pass_counter += 1
58 # if passed_seqs.find_by_name_start( hmmscan_data.seq_name, true ).length < 1
59 # add_sequence( hmmscan_data.seq_name, in_msa, passed_seqs )
60 # proteins_with_passing_domains += 1
66 extract_domain( sequence,
81 if sequence != prev_sequence
84 if ( env_from - prev_env_to ) <= min_linker
85 extract_domain( sequence,
86 prev_number.to_s + "+" + number.to_s,
99 close_pairs_counter += 2
102 extract_domain( sequence,
108 out_msa_distant_partners,
115 distant_pairs_counter += 1
118 extract_domain( sequence,
124 out_msa_distant_partners,
131 distant_pairs_counter += 1
135 end # sequence != prev_sequence else
137 prev_sequence = sequence
139 prev_env_from = env_from
141 #prev_i_e_value = i_e_value
147 end # def process_hmmscan_data
150 # raises ArgumentError, IOError, StandardError
151 def parse( domain_id,
161 add_domain_number_as_digit,
162 add_domain_number_as_letter,
168 Util.check_file_for_readability( hmmscan_output )
169 Util.check_file_for_readability( fasta_sequence_file )
170 Util.check_file_for_writability( outfile )
171 Util.check_file_for_writability( passed_seqs_outfile )
172 Util.check_file_for_writability( failed_seqs_outfile )
175 factory = MsaFactory.new()
176 in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
178 if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
179 error_msg = "could not find fasta sequences in " + fasta_sequence_file
180 raise IOError, error_msg
185 failed_seqs = Msa.new
186 passed_seqs = Msa.new
188 out_msa_distant_partners = nil
189 out_msa_singlets = nil
191 out_msa_pairs = Msa.new
192 out_msa_distant_partners = Msa.new
193 out_msa_singlets = Msa.new
196 ld = Constants::LINE_DELIMITER
198 domain_pass_counter = 0
199 domain_fail_counter = 0
201 distant_pairs_counter = 0
202 close_pairs_counter = 0
203 proteins_with_passing_domains = 0
204 proteins_with_failing_domains = 0
205 max_domain_copy_number_per_protein = -1
206 max_domain_copy_number_sequence = ""
212 # prev_i_e_value = nil
216 hmmscan_datas = Array.new
219 File.open( hmmscan_output ) do | file |
220 while line = file.gets
221 if !is_ignorable?( line ) && line =~ /^\S+\s+/
223 # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
224 # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
225 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+(.*)/
238 if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
239 ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
240 hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
241 if ( number > max_domain_copy_number_per_protein )
242 max_domain_copy_number_sequence = sequence
243 max_domain_copy_number_per_protein = number
246 print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
247 log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
248 if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
249 print( " iE=" + i_e_value.to_s )
250 log << " iE=" + i_e_value.to_s
252 if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
253 le = env_to - env_from + 1
254 print( " l=" + le.to_s )
255 log << " l=" + le.to_s
259 domain_fail_counter += 1
261 if failed_seqs.find_by_name_start( sequence, true ).length < 1
262 add_sequence( sequence, in_msa, failed_seqs )
263 proteins_with_failing_domains += 1
268 error_msg = "number > out_of ! (this should not have happened)"
269 raise StandardError, error_msg
272 if number == out_of && !hmmscan_datas.empty?
273 domain_pass_counter += process_hmmscan_datas( hmmscan_datas,
285 end # while line = file.gets
286 end # File.open( hmmsearch_output ) do | file |
290 if domain_pass_counter < 1
291 error_msg = "no domain sequences were extracted"
292 raise IOError, error_msg
296 puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
297 log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
300 if ( max_domain_copy_number_per_protein > 1 )
301 puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
302 log << "First protein with this copy number: " + max_domain_copy_number_sequence
306 write_msa( out_msa, outfile )
307 write_msa( passed_seqs, passed_seqs_outfile )
308 write_msa( failed_seqs, failed_seqs_outfile )
311 write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s )
315 write_msa( out_msa_singlets, outfile +"_singles" )
318 if out_msa_distant_partners
319 write_msa( out_msa_distant_partners, outfile + "_" + min_linker.to_s + "_isolated" );
324 log << "passing domains : " + domain_pass_counter.to_s + ld
326 log << "single domains : " + singlets_counter.to_s + ld
327 log << "domains in close pairs : " + close_pairs_counter.to_s + ld
328 log << "isolated domains : " + distant_pairs_counter.to_s + ld
330 log << "failing domains : " + domain_fail_counter.to_s + ld
331 log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld
332 log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
335 return domain_pass_counter
342 def write_msa( msa, filename )
344 w = FastaWriter.new()
345 w.set_line_width( 60 )
348 io.write_to_file( msa, filename, w )
350 error_msg = "could not write to \"" + filename + "\""
351 raise IOError, error_msg
356 def add_sequence( sequence_name, in_msa, add_to_msa )
357 seqs = in_msa.find_by_name_start( sequence_name, true )
358 if ( seqs.length < 1 )
359 error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
360 raise StandardError, error_msg
362 if ( seqs.length > 1 )
363 error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
364 raise StandardError, error_msg
366 seq = in_msa.get_sequence( seqs[ 0 ] )
367 add_to_msa.add_sequence( seq )
371 def extract_domain( sequence,
382 if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
383 error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
384 raise StandardError, error_msg
386 if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
387 error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
388 raise StandardError, error_msg
390 seqs = in_msa.find_by_name_start( sequence, true )
392 error_msg = "sequence \"" + sequence + "\" not found in sequence file"
393 raise IOError, error_msg
396 error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
397 raise IOError, error_msg
399 # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
400 seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
402 orig_name = seq.get_name
404 seq.set_name( orig_name.split[ 0 ] )
407 seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
411 seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] )
414 if out_of != 1 && add_domain_number
415 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
419 a = orig_name.rindex "["
420 b = orig_name.rindex "]"
422 error_msg = "species not found in " + orig_name
423 raise StandardError, error_msg
425 species = orig_name[ a .. b ]
426 seq.set_name( seq.get_name + " " + species )
428 out_msa.add_sequence( seq )
431 def is_ignorable?( line )
432 return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
435 end # class HmmscanDomainExtractor
438 def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
444 @i_e_value = i_e_value
446 attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value