From 07ac6e752b2d6e466fa350a46fd2a3c89b7ca034 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 29 Sep 2012 05:01:34 +0000 Subject: [PATCH] in progress --- .../lib/evo/io/parser/hmmscan_domain_extractor.rb | 265 ++++++++++---------- 1 file changed, 132 insertions(+), 133 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb index 273f348..865424b 100644 --- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb @@ -138,7 +138,7 @@ module Evoruby if sequence != prev_sequence prev_is_pair = false end - + if out_of == 1 if sequence == prev_sequence @@ -240,169 +240,168 @@ module Evoruby end end end - end - end + end # if !is_ignorable?( line ) && line =~ /^\S+\s+/ + end # while line = file.gets + end # File.open( hmmsearch_output ) do | file | - if domain_pass_counter < 1 - error_msg = "no domain sequences were extracted" - raise StandardError, error_msg - end + if domain_pass_counter < 1 + error_msg = "no domain sequences were extracted" + raise StandardError, error_msg + end - log << Constants::LINE_DELIMITER - puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s ) - log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s - log << Constants::LINE_DELIMITER + log << Constants::LINE_DELIMITER + puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s ) + log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s + log << Constants::LINE_DELIMITER - if ( max_domain_copy_number_per_protein > 1 ) - puts( "First protein with this copy number: " + max_domain_copy_number_sequence ) - log << "First protein with this copy number: " + max_domain_copy_number_sequence - log << Constants::LINE_DELIMITER - end + if ( max_domain_copy_number_per_protein > 1 ) + puts( "First protein with this copy number: " + max_domain_copy_number_sequence ) + log << "First protein with this copy number: " + max_domain_copy_number_sequence + log << Constants::LINE_DELIMITER + end - write_msa( out_msa, outfile ) - write_msa( passed_seqs, passed_seqs_outfile ) - write_msa( failed_seqs, failed_seqs_outfile ) + write_msa( out_msa, outfile ) + write_msa( passed_seqs, passed_seqs_outfile ) + write_msa( failed_seqs, failed_seqs_outfile ) - if out_msa_pairs - write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s ) - end + if out_msa_pairs + write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s ) + end - if out_msa_singlets - write_msa( out_msa_singlets, outfile +"_singles" ) - end + if out_msa_singlets + write_msa( out_msa_singlets, outfile +"_singles" ) + end - if out_msa_distant_partners - write_msa( out_msa_distant_partners, outfile +"_singles" ) - end + if out_msa_distant_partners + write_msa( out_msa_distant_partners, outfile +"_singles" ) + end - log << ld - log << "passing domains : " + domain_pass_counter.to_s + ld - log << "failing domains : " + domain_fail_counter.to_s + ld - log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld - log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld - log << ld + log << ld + log << "passing domains : " + domain_pass_counter.to_s + ld + log << "failing domains : " + domain_fail_counter.to_s + ld + log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld + log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld + log << ld - return domain_pass_counter + return domain_pass_counter - end # parse + end # parse - private + private - def write_msa( msa, filename ) - io = MsaIO.new() - w = FastaWriter.new() - w.set_line_width( 60 ) - w.clean( true ) - begin - io.write_to_file( msa, filename, w ) - rescue Exception - error_msg = "could not write to \"" + filename + "\"" - raise IOError, error_msg - end + def write_msa( msa, filename ) + io = MsaIO.new() + w = FastaWriter.new() + w.set_line_width( 60 ) + w.clean( true ) + begin + io.write_to_file( msa, filename, w ) + rescue Exception + error_msg = "could not write to \"" + filename + "\"" + raise IOError, error_msg end + end - def add_sequence( sequence_name, in_msa, add_to_msa ) - seqs = in_msa.find_by_name_start( sequence_name, true ) - if ( seqs.length < 1 ) - error_msg = "sequence \"" + sequence_name + "\" not found in sequence file" - raise StandardError, error_msg - end - if ( seqs.length > 1 ) - error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file" - raise StandardError, error_msg - end - seq = in_msa.get_sequence( seqs[ 0 ] ) - add_to_msa.add_sequence( seq ) + def add_sequence( sequence_name, in_msa, add_to_msa ) + seqs = in_msa.find_by_name_start( sequence_name, true ) + if ( seqs.length < 1 ) + error_msg = "sequence \"" + sequence_name + "\" not found in sequence file" + raise StandardError, error_msg end + if ( seqs.length > 1 ) + error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file" + raise StandardError, error_msg + end + seq = in_msa.get_sequence( seqs[ 0 ] ) + add_to_msa.add_sequence( seq ) + end - # raises ArgumentError, StandardError - def extract_domain( sequence, - number, - out_of, - seq_from, - seq_to, - in_msa, - out_msa, - add_position, - add_domain_number, - add_domain_number_as_digit, - add_domain_number_as_letter, - trim_name, - add_species ) - if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of ) - error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s - raise ArgumentError, error_msg - end - if seq_from < 1 || seq_to < 1 || seq_from >= seq_to - error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s - raise ArgumentError, error_msg - end - seqs = in_msa.find_by_name_start( sequence, true ) - if seqs.length < 1 - error_msg = "sequence \"" + sequence + "\" not found in sequence file" - raise StandardError, error_msg - end - if seqs.length > 1 - error_msg = "sequence \"" + sequence + "\" not unique in sequence file" - raise StandardError, error_msg - end - # hmmsearch is 1 based, wheres sequences are 0 bases in this package. - seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 ) - - orig_name = seq.get_name - - seq.set_name( orig_name.split[ 0 ] ) + # raises ArgumentError, StandardError + def extract_domain( sequence, + number, + out_of, + seq_from, + seq_to, + in_msa, + out_msa, + add_position, + add_domain_number, + add_domain_number_as_digit, + add_domain_number_as_letter, + trim_name, + add_species ) + if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of ) + error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s + raise ArgumentError, error_msg + end + if seq_from < 1 || seq_to < 1 || seq_from >= seq_to + error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s + raise ArgumentError, error_msg + end + seqs = in_msa.find_by_name_start( sequence, true ) + if seqs.length < 1 + error_msg = "sequence \"" + sequence + "\" not found in sequence file" + raise StandardError, error_msg + end + if seqs.length > 1 + error_msg = "sequence \"" + sequence + "\" not unique in sequence file" + raise StandardError, error_msg + end + # hmmsearch is 1 based, wheres sequences are 0 bases in this package. + seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 ) - if add_position - seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s ) - end + orig_name = seq.get_name - if trim_name - seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] ) - end + seq.set_name( orig_name.split[ 0 ] ) - if out_of != 1 - if add_domain_number_as_digit - seq.set_name( seq.get_name + number.to_s ) - elsif add_domain_number_as_letter - if number > 25 - error_msg = 'too many identical domains per sequence, cannot use letters to distinguish them' - raise StandardError, error_msg - end - seq.set_name( seq.get_name + ( number + 96 ).chr ) - elsif add_domain_number - seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s ) - end - end + if add_position + seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s ) + end - # if ( seq.get_name.length > 10 ) - # error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters" - # raise StandardError, error_msg - # end + if trim_name + seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] ) + end - if add_species - a = orig_name.rindex "[" - b = orig_name.rindex "]" - unless a && b - error_msg = "species not found in " + orig_name + if out_of != 1 + if add_domain_number_as_digit + seq.set_name( seq.get_name + number.to_s ) + elsif add_domain_number_as_letter + if number > 25 + error_msg = 'too many identical domains per sequence, cannot use letters to distinguish them' raise StandardError, error_msg end - species = orig_name[ a .. b ] - seq.set_name( seq.get_name + " " + species ) + seq.set_name( seq.get_name + ( number + 96 ).chr ) + elsif add_domain_number + seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s ) end + end - out_msa.add_sequence( seq ) + # if ( seq.get_name.length > 10 ) + # error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters" + # raise StandardError, error_msg + # end + if add_species + a = orig_name.rindex "[" + b = orig_name.rindex "]" + unless a && b + error_msg = "species not found in " + orig_name + raise StandardError, error_msg + end + species = orig_name[ a .. b ] + seq.set_name( seq.get_name + " " + species ) end + out_msa.add_sequence( seq ) + end - def is_ignorable?( line ) - return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ ) - end + def is_ignorable?( line ) + return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ ) + end - end # class HmmscanDomainExtractor + end # class HmmscanDomainExtractor - end # module Evoruby +end # module Evoruby -- 1.7.10.2