X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Fio%2Fparser%2Fhmmscan_domain_extractor.rb;h=0a7f2b16b8aae25a2a20c1f6857ff428becf8882;hb=aa35322a551ab7813ee845799d64830a986a3fae;hp=30962da9ade3f56690e70ba076c0891bdb768208;hpb=4832d54fed791f182d012d406e4bcebefef0547c;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 30962da..0a7f2b1 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 @@ -1,11 +1,10 @@ # # = 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: 2017/02/20 require 'lib/evo/util/constants' require 'lib/evo/msa/msa_factory' @@ -14,29 +13,27 @@ 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 + ADD_TO_CLOSE_PAIRS = 0 def initialize end # raises ArgumentError, IOError, StandardError def parse( domain_id, - 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 ) + 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 ) @@ -80,76 +77,136 @@ module Evoruby ld = Constants::LINE_DELIMITER - domain_pass_counter = 0 - domain_fail_counter = 0 - proteins_with_failing_domains = 0 + domain_pass_counter = 0 + domain_fail_counter = 0 + passing_domains_per_protein = 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 = "" + passing_target_length_sum = 0 + overall_target_length_sum = 0 + overall_target_length_min = 10000000 + overall_target_length_max = -1 + passing_target_length_min = 10000000 + passing_target_length_max = -1 + + overall_target_ie_min = 10000000 + overall_target_ie_max = -1 + passing_target_ie_min = 10000000 + passing_target_ie_max = -1 hmmscan_datas = [] hmmscan_parser = HmmscanParser.new( hmmscan_output ) results = hmmscan_parser.parse + prev_query = nil + saw_target = false + results.each do | r | + + if ( prev_query != nil ) && ( r.query != prev_query ) + protein_counter += 1 + passing_domains_per_protein = 0 + 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 = 1 + env_to - env_from + + 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 i_e_value > overall_target_ie_max + overall_target_ie_max = i_e_value + end + if i_e_value < overall_target_ie_min + overall_target_ie_min = i_e_value + end if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) && - ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) ) + ( ( length_threshold <= 0 ) || ( length >= length_threshold.to_f ) ) ) hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value ) - if ( number > max_domain_copy_number_per_protein ) + passing_target_length_sum += length + passing_domains_per_protein += 1 + 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 i_e_value > passing_target_ie_max + passing_target_ie_max = i_e_value + end + if i_e_value < passing_target_ie_min + passing_target_ie_min = i_e_value + end + if ( passing_domains_per_protein > max_domain_copy_number_per_protein ) max_domain_copy_number_sequence = sequence - max_domain_copy_number_per_protein = number + max_domain_copy_number_per_protein = passing_domains_per_protein end - else # failed - 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)" + 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 ) ) - 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( ld ) log << ld - domain_fail_counter += 1 + domain_fail_counter += 1 end if number > out_of - error_msg = "number > out_of ! (this should not have happened)" + 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 ) + 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 ) @@ -157,7 +214,7 @@ module Evoruby error_msg = "this should not have happened" raise StandardError, error_msg end - else + 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 @@ -168,6 +225,12 @@ module Evoruby 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 @@ -175,14 +238,59 @@ module Evoruby 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 + + 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 iE: min-max: " + passing_target_ie_min.to_s + " - " + passing_target_ie_max.to_s) + log << "Passing target domain iE: min-max: " + passing_target_ie_min.to_s + " - " + passing_target_ie_max.to_s + log << ld + puts( "Passing target domains: sum: " + domain_pass_counter.to_s ) + log << "Passing target domains: 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( "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 + 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 target domain iE: min-max: " + overall_target_ie_min.to_s + " - " + overall_target_ie_max.to_s) + log << "All target target domain iE: min-max: " + overall_target_ie_min.to_s + " - " + overall_target_ie_max.to_s + log << ld + puts( "All target domains: sum: " + sum.to_s ) + log << "All target domains: 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: " + max_domain_copy_number_per_protein.to_s ) + log << "Max target domain copy number per protein: " + 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 + 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 @@ -191,11 +299,11 @@ module Evoruby write_msa( failed_seqs, failed_seqs_outfile ) if out_msa_pairs - write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta") + write_msa( out_msa_pairs, outfile + "_" + min_linker.to_s + ".fasta") end if out_msa_singles - write_msa( out_msa_singles, outfile +"_singles.fasta") + write_msa( out_msa_singles, outfile + "_singles.fasta") end if out_msa_isolated @@ -203,7 +311,7 @@ module Evoruby end if out_msa_single_domains_protein_seqs - write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" ) + write_msa( out_msa_single_domains_protein_seqs, outfile + "_proteins_with_singles.fasta" ) end if out_msa_close_pairs_protein_seqs @@ -228,31 +336,33 @@ module Evoruby 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 + 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 << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld - log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld - log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + 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 wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld + 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 @@ -261,7 +371,6 @@ module Evoruby end # parse - private def write_msa( msa, filename ) @@ -277,7 +386,6 @@ module Evoruby 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 ) @@ -293,21 +401,21 @@ module Evoruby end 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 ) + 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 @@ -325,28 +433,28 @@ module Evoruby 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_species ) + index + 1, + actual_out_of, + hmmscan_data.env_from, + hmmscan_data.env_to, + in_msa, + out_msa, + add_position, + add_domain_number, + add_species ) 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 ) + 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 @@ -359,33 +467,50 @@ module Evoruby 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 ) ) ) + ( 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 ) + 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, - hmmscan_datas[ index - 1 ].env_from, - hmmscan_data.env_to, - in_msa, - out_msa_pairs, - add_position, - add_domain_number, - add_species ) + 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 @@ -437,21 +562,21 @@ module Evoruby 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 = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s + 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-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s + 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 ) @@ -463,7 +588,7 @@ module Evoruby error_msg = "sequence \"" + sequence + "\" not unique in sequence file" 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