X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Fio%2Fparser%2Fhmmscan_domain_extractor.rb;h=89e0fe7dd8883eb15f6a9e25912c689685c71558;hb=2a165043be7f54dc4445bf4332a1af5283711fdf;hp=8032a283d31c7ef7a4de8f9e1c654f801abb8605;hpb=87c745e122b46fad66e38857a1dd7f82323a9d40;p=jalview.git 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 8032a28..89e0fe7 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 @@ -1,48 +1,43 @@ # # = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class # -# Copyright:: Copyright (C) 2012 Christian M. Zmasek -# License:: GNU Lesser General Public License (LGPL) +# Copyright:: Copyright (C) 2017 Christian M. Zmasek +# License:: GNU Lesser General Public License (LGPL) # -# $Id: $ - +# Last modified: 2017/02/16 require 'lib/evo/util/constants' require 'lib/evo/msa/msa_factory' require 'lib/evo/io/msa_io' require 'lib/evo/io/writer/fasta_writer' require 'lib/evo/io/parser/fasta_parser' - +require 'lib/evo/io/parser/hmmscan_parser' module Evoruby - class HmmscanDomainExtractor - TRIM_BY = 2 - + ADD_TO_CLOSE_PAIRS = 0 def initialize end # raises ArgumentError, IOError, StandardError def parse( domain_id, - hmmsearch_output, - fasta_sequence_file, - outfile, - passed_seqs_outfile, - failed_seqs_outfile, - e_value_threshold, - length_threshold, - add_position, - add_domain_number, - add_domain_number_as_digit, - add_domain_number_as_letter, - trim_name, - add_species, - log ) - - Util.check_file_for_readability( hmmsearch_output ) + hmmscan_output, + fasta_sequence_file, + outfile, + passed_seqs_outfile, + failed_seqs_outfile, + e_value_threshold, + length_threshold, + add_position, + add_domain_number, + add_species, + min_linker, + log ) + + Util.check_file_for_readability( hmmscan_output ) Util.check_file_for_readability( fasta_sequence_file ) - Util.check_file_for_writability( outfile ) + Util.check_file_for_writability( outfile + ".fasta" ) Util.check_file_for_writability( passed_seqs_outfile ) Util.check_file_for_writability( failed_seqs_outfile ) @@ -56,150 +51,313 @@ module Evoruby end out_msa = Msa.new + failed_seqs = Msa.new passed_seqs = Msa.new + out_msa_pairs = nil + out_msa_isolated = nil + out_msa_singles = nil + out_msa_single_domains_protein_seqs = nil + out_msa_close_pairs_protein_seqs = nil + out_msa_close_pairs_only_protein_seqs = nil + out_msa_isolated_protein_seqs = nil + out_msa_isolated_only_protein_seqs = nil + out_msa_isolated_and_close_pair_protein_seqs = nil + if min_linker + out_msa_pairs = Msa.new + out_msa_isolated = Msa.new + out_msa_singles = Msa.new + out_msa_single_domains_protein_seqs = Msa.new + out_msa_close_pairs_protein_seqs = Msa.new + out_msa_close_pairs_only_protein_seqs = Msa.new + out_msa_isolated_protein_seqs = Msa.new + out_msa_isolated_only_protein_seqs = Msa.new + out_msa_isolated_and_close_pair_protein_seqs = Msa.new + end ld = Constants::LINE_DELIMITER - domain_pass_counter = 0 - domain_fail_counter = 0 - proteins_with_passing_domains = 0 - proteins_with_failing_domains = 0 + domain_pass_counter = 0 + domain_fail_counter = 0 + proteins_with_failing_domains = 0 + domain_not_present_counter = 0 + protein_counter = 1 max_domain_copy_number_per_protein = -1 - max_domain_copy_number_sequence = '' - failed_species_counts = Hash.new - passed_species_counts = Hash.new + max_domain_copy_number_sequence = "" + passing_target_length_sum = 0 + overall_target_length_sum = 0 + overall_target_length_min = 10000000 + overall_target_length_max = 0 + passing_target_length_min = 10000000 + passing_target_length_max = 0 - File.open( hmmsearch_output ) do | file | - while line = file.gets - if !is_ignorable?( line ) && line =~ /^\S+\s+/ + hmmscan_datas = [] - # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc - # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 - 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+(.*)/ + hmmscan_parser = HmmscanParser.new( hmmscan_output ) + results = hmmscan_parser.parse - target_name = $1 - if domain_id != target_name - next - end + prev_query = nil + saw_target = false + + results.each do | r | + + if ( prev_query != nil ) && ( r.query != prev_query ) + protein_counter += 1 + if !saw_target + log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld + domain_not_present_counter += 1 + end + saw_target = false + end + + prev_query = r.query + + if domain_id != r.model + next + end + + saw_target = true + + sequence = r.query + number = r.number + out_of = r.out_of + env_from = r.env_from + env_to = r.env_to + i_e_value = r.i_e_value + prev_query = r.query + length = env_to - env_from + 1 - sequence = $4 - number = $10.to_i - out_of = $11.to_i - env_from = $20.to_i - env_to = $21.to_i - i_e_value = $13.to_f - if ( number > max_domain_copy_number_per_protein ) - max_domain_copy_number_sequence = sequence - max_domain_copy_number_per_protein = number + overall_target_length_sum += length + if length > overall_target_length_max + overall_target_length_max = length + end + if length < overall_target_length_min + overall_target_length_min = length + end + + if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) && + ( ( length_threshold <= 0 ) || ( length >= length_threshold.to_f ) ) ) + hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value ) + passing_target_length_sum += length + if length > passing_target_length_max + passing_target_length_max = length + end + if length < passing_target_length_min + passing_target_length_min = length + end + if ( number > max_domain_copy_number_per_protein ) + max_domain_copy_number_sequence = sequence + max_domain_copy_number_per_protein = number + end + else # no pass + log << domain_fail_counter.to_s + ": " + sequence.to_s + " fails threshold(s)" + if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) ) + log << " iE=" + i_e_value.to_s + end + if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f ) + le = env_to - env_from + 1 + log << " l=" + le.to_s + end + log << ld + domain_fail_counter += 1 + end + + if number > out_of + error_msg = "number > out_of (this should not have happened)" + raise StandardError, error_msg + end + + if number == out_of + if !hmmscan_datas.empty? + process_hmmscan_datas( hmmscan_datas, + in_msa, + add_position, + add_domain_number, + add_species, + out_msa, + out_msa_singles, + out_msa_pairs, + out_msa_isolated, + min_linker, + out_msa_single_domains_protein_seqs, + out_msa_close_pairs_protein_seqs, + out_msa_close_pairs_only_protein_seqs, + out_msa_isolated_protein_seqs, + out_msa_isolated_only_protein_seqs, + out_msa_isolated_and_close_pair_protein_seqs ) + domain_pass_counter += hmmscan_datas.length + if passed_seqs.find_by_name_start( sequence, true ).length < 1 + add_sequence( sequence, in_msa, passed_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg end - if ( ( ( e_value_threshold.to_f < 0.0 ) || ( i_e_value <= e_value_threshold ) ) && - ( ( length_threshold.to_f <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) ) - extract_domain( sequence, - number, - out_of, - env_from, - env_to, - in_msa, - out_msa, - add_position, - add_domain_number, - add_domain_number_as_digit, - add_domain_number_as_letter, - trim_name , - add_species ) - domain_pass_counter += 1 - count_species( sequence, passed_species_counts ) - if passed_seqs.find_by_name_start( sequence, true ).length < 1 - add_sequence( sequence, in_msa, passed_seqs ) - proteins_with_passing_domains += 1 - end + else # no pass + if failed_seqs.find_by_name_start( sequence, true ).length < 1 + add_sequence( sequence, in_msa, failed_seqs ) + proteins_with_failing_domains += 1 else - print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" ) - log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" - if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) ) - print( " iE=" + i_e_value.to_s ) - log << " iE=" + i_e_value.to_s - end - if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f ) - le = env_to - env_from + 1 - print( " l=" + le.to_s ) - log << " l=" + le.to_s - end - print( Constants::LINE_DELIMITER ) - log << Constants::LINE_DELIMITER - domain_fail_counter += 1 - count_species( sequence, failed_species_counts ) - if failed_seqs.find_by_name_start( sequence, true ).length < 1 - add_sequence( sequence, in_msa, failed_seqs ) - proteins_with_failing_domains += 1 - end + error_msg = "this should not have happened" + raise StandardError, error_msg end end + hmmscan_datas.clear end + + end # results.each do | r | + + if (prev_query != nil) && (!saw_target) + log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld + domain_not_present_counter += 1 end if domain_pass_counter < 1 error_msg = "no domain sequences were extracted" + raise IOError, error_msg + end + + if ( domain_not_present_counter + passed_seqs.get_number_of_seqs + proteins_with_failing_domains ) != protein_counter + error_msg = "not present + passing + not passing != proteins in sequence (fasta) file (this should not have happened)" 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 + puts + log << ld + + log << ld + avg_pass = ( passing_target_length_sum / domain_pass_counter ) + puts( "Passing target domain lengths: average: " + avg_pass.to_s ) + log << "Passing target domain lengths: average: " + avg_pass.to_s + log << ld + puts( "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s) + log << "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s + log << ld + puts( "Passing target domain lengths: sum: " + domain_pass_counter.to_s ) + log << "Passing target domain lengths: sum: " + domain_pass_counter.to_s + log << ld + log << ld + puts + sum = domain_pass_counter + domain_fail_counter + avg_all = overall_target_length_sum / sum + puts( "All target domain lengths: average: " + avg_all.to_s ) + log << "All target domain lengths: average: " +avg_all.to_s + log << ld + puts( "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s) + log << "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s + log << ld + puts( "All target domain lengths: sum: " + sum.to_s ) + log << "All target domain lengths: sum: " + sum.to_s + + puts + puts( "Proteins with passing target domain(s): " + passed_seqs.get_number_of_seqs.to_s ) + puts( "Proteins with no passing target domain: " + proteins_with_failing_domains.to_s ) + puts( "Proteins with no target domain : " + domain_not_present_counter.to_s ) + + log << ld + log << ld + puts + puts( "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s ) + log << "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s + log << ld 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 + puts( "First target protein with this copy number: " + max_domain_copy_number_sequence ) + log << "First target protein with this copy number: " + max_domain_copy_number_sequence + log << ld end - io = MsaIO.new() - w = FastaWriter.new() - w.set_line_width( 60 ) - w.clean( true ) + write_msa( out_msa, outfile + ".fasta" ) + write_msa( passed_seqs, passed_seqs_outfile ) + write_msa( failed_seqs, failed_seqs_outfile ) - begin - io.write_to_file( out_msa, outfile, w ) - rescue Exception - error_msg = "could not write to \"" + outfile + "\"" - raise IOError, error_msg + if out_msa_pairs + write_msa( out_msa_pairs, outfile + "_" + min_linker.to_s + ".fasta") end - begin - io.write_to_file( passed_seqs, passed_seqs_outfile, w ) - rescue Exception - error_msg = "could not write to \"" + passed_seqs_outfile + "\"" - raise IOError, error_msg + if out_msa_singles + write_msa( out_msa_singles, outfile + "_singles.fasta") end - begin - io.write_to_file( failed_seqs, failed_seqs_outfile, w ) - rescue Exception - error_msg = "could not write to \"" + failed_seqs_outfile + "\"" - raise IOError, error_msg + if out_msa_isolated + write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta"); + end + + if out_msa_single_domains_protein_seqs + write_msa( out_msa_single_domains_protein_seqs, outfile + "_proteins_with_singles.fasta" ) + end + + if out_msa_close_pairs_protein_seqs + write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" ) + end + + if out_msa_close_pairs_only_protein_seqs + write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" ) + end + + if out_msa_isolated_protein_seqs + write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" ) + end + + if out_msa_isolated_only_protein_seqs + write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" ) + end + + if out_msa_isolated_and_close_pair_protein_seqs + write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" ) + end + + if min_linker + if ( out_msa_single_domains_protein_seqs.get_number_of_seqs + + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs + + out_msa_isolated_only_protein_seqs.get_number_of_seqs + + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs + error_msg = "this should not have happened" + raise StandardError, error_msg + end 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 << 'passing domains counts per species: ' << ld - passed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld } - log << ld - log << 'failing domains counts per species: ' << ld - failed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld } + log << "passing target domains : " + domain_pass_counter.to_s + ld + log << "failing target domains : " + domain_fail_counter.to_s + ld + log << "proteins in sequence (fasta) file : " + in_msa.get_number_of_seqs.to_s + ld + log << "proteins in hmmscan outputfile : " + protein_counter.to_s + ld + log << "proteins with passing target domain(s) : " + passed_seqs.get_number_of_seqs.to_s + ld + log << "proteins with no passing target domain : " + proteins_with_failing_domains.to_s + ld + log << "proteins with no target domain : " + domain_not_present_counter.to_s + ld + if min_linker + log << "min linker length : " + min_linker.to_s + ld + log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld + log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld + log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld + log << "proteins with single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld + end + log << ld + return domain_pass_counter end # parse 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 + end def add_sequence( sequence_name, in_msa, add_to_msa ) seqs = in_msa.find_by_name_start( sequence_name, true ) @@ -215,38 +373,195 @@ module Evoruby add_to_msa.add_sequence( seq ) end - # raises ArgumentError, StandardError - def extract_domain( sequence, - number, - out_of, - seq_from, - seq_to, + def process_hmmscan_datas( hmmscan_datas, + in_msa, + add_position, + add_domain_number, + add_species, + out_msa, + out_msa_singles, + out_msa_pairs, + out_msa_isolated, + min_linker, + out_msa_single_domains_protein_seqs, + out_msa_close_pairs_protein_seqs, + out_msa_close_pairs_only_protein_seqs, + out_msa_isolated_protein_seqs, + out_msa_isolated_only_protein_seqs, + out_msa_isolated_and_close_pair_protein_seqs ) + + actual_out_of = hmmscan_datas.size + saw_close_pair = false + saw_isolated = false + + seq_name = "" + prev_seq_name = nil + + hmmscan_datas.each_with_index do |hmmscan_data, index| + if hmmscan_data.number < ( index + 1 ) + error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)" + raise StandardError, error_msg + end + + seq_name = hmmscan_data.seq_name + + extract_domain( seq_name, + index + 1, + actual_out_of, + hmmscan_data.env_from, + hmmscan_data.env_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 < 1 || out_of < 1 || number > out_of ) - error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s - raise ArgumentError, error_msg + + if min_linker + if actual_out_of == 1 + extract_domain( seq_name, + 1, + 1, + hmmscan_data.env_from, + hmmscan_data.env_to, + in_msa, + out_msa_singles, + add_position, + add_domain_number, + add_species ) + if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end + + else + first = index == 0 + last = index == hmmscan_datas.length - 1 + + if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) || + ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) || + ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) && + ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ) + + extract_domain( seq_name, + index + 1, + actual_out_of, + hmmscan_data.env_from, + hmmscan_data.env_to, + in_msa, + out_msa_isolated, + add_position, + add_domain_number, + add_species ) + saw_isolated = true + + elsif !first + + from = hmmscan_datas[ index - 1 ].env_from + to = hmmscan_data.env_to + + if ADD_TO_CLOSE_PAIRS > 0 + from = from - ADD_TO_CLOSE_PAIRS + if from < 1 + from = 1 + end + to = to + ADD_TO_CLOSE_PAIRS + temp_seqs = in_msa.find_by_name_start( seq_name, true ) + temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] ) + if to > temp_seq.get_length + to = temp_seq.get_length + end + end + + extract_domain( seq_name, + index.to_s + "+" + ( index + 1 ).to_s, + actual_out_of, + from, + to, + in_msa, + out_msa_pairs, + add_position, + add_domain_number, + add_species ) + saw_close_pair = true + end + end + end + if prev_seq_name && prev_seq_name != seq_name + error_msg = "this should not have happened" + raise StandardError, error_msg + end + prev_seq_name = seq_name + end # each + if saw_isolated + if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end 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 + if saw_close_pair + if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end + end + if saw_close_pair && saw_isolated + if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end + elsif saw_close_pair + if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end + elsif saw_isolated + if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1 + add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs ) + else + error_msg = "this should not have happened" + raise StandardError, error_msg + end + end + end # def process_hmmscan_data + + def extract_domain( sequence, + number, + out_of, + seq_from, + seq_to, + in_msa, + out_msa, + add_position, + add_domain_number, + add_species ) + if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of ) + error_msg = "number=" + number.to_s + ", out of=" + out_of.to_s + raise StandardError, error_msg + end + if seq_from < 1 || seq_to < 1 || seq_from >= seq_to + error_msg = "impossible: seq-from=" + seq_from.to_s + ", seq-to=" + seq_to.to_s + raise StandardError, 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 + raise IOError, error_msg end if seqs.length > 1 error_msg = "sequence \"" + sequence + "\" not unique in sequence file" - raise StandardError, error_msg + raise IOError, error_msg end - # hmmsearch is 1 based, wheres sequences are 0 bases in this package. + # hmmscan is 1 based, whereas 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 @@ -257,68 +572,40 @@ module Evoruby seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s ) end - if trim_name - seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] ) + if out_of != 1 && add_domain_number + seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s ) end - 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 - - 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 + "]" ) + 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 - - # if ( seq.get_name.length > 10 ) - # error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters" - # raise StandardError, error_msg - # end - out_msa.add_sequence( seq ) end - def count_species( sequence, species_counts_map ) - species = get_species( sequence ) - if species != nil - if !species_counts_map.has_key?( species ) - species_counts_map[ species ] = 1 - else - species_counts_map[ species ] = species_counts_map[ species ] + 1 - end - end - end - - def get_species( sequence_name ) - if sequence_name =~ /^.+_(.+)$/ - return $1 - else - return nil - end - end - def is_ignorable?( line ) return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ ) end end # class HmmscanDomainExtractor + class HmmsearchData + def initialize( seq_name, number, out_of, env_from, env_to, i_e_value ) + @seq_name = seq_name + @number = number + @out_of = out_of + @env_from = env_from + @env_to = env_to + @i_e_value = i_e_value + end + attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value + end + end # module Evoruby