From: cmzmasek Date: Sat, 25 Feb 2017 01:26:11 +0000 (-0800) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=82c56a39596009de42d64b85390f2b6bc03663b9;p=jalview.git in progress... --- diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_multi_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_multi_domain_extractor.rb index 89b4856..56bf65f 100644 --- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_multi_domain_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_multi_domain_extractor.rb @@ -85,10 +85,10 @@ module Evoruby #### # Import: if multiple copies of same domain, threshold need to be same! target_domain_ary = Array.new - target_domain_ary.push(TargetDomain.new('Hexokinase_1', 0.1, -1, 0.5, 1 )) - target_domain_ary.push(TargetDomain.new('Hexokinase_2', 0.1, -1, 0.5, 1 )) - target_domain_ary.push(TargetDomain.new('Hexokinase_2', 0.1, -1, 0.5, 1 )) - target_domain_ary.push(TargetDomain.new('Hexokinase_1', 0.1, -1, 0.5, 1 )) + target_domain_ary.push(TargetDomain.new('Hexokinase_1', 1e-6, -1, 0.6, 1 )) + target_domain_ary.push(TargetDomain.new('Hexokinase_2', 1e-6, -1, 0.6, 1 )) + # target_domain_ary.push(TargetDomain.new('Hexokinase_2', 0.1, -1, 0.5, 1 )) + # target_domain_ary.push(TargetDomain.new('Hexokinase_1', 0.1, -1, 0.5, 1 )) #target_domain_ary.push(TargetDomain.new('BH4', 0.1, -1, 0.5, 0 )) #target_domain_ary.push(TargetDomain.new('Bcl-2', 0.1, -1, 0.5, 1 )) @@ -124,9 +124,11 @@ module Evoruby passing_sequences = Array.new total_sequences = 0 @passed = Hash.new + out_domain_msas = Hash.new + out_domain_architecture_msa = Msa.new results.each do |hmmscan_result| if ( prev_query_seq_name != nil ) && ( hmmscan_result.query != prev_query_seq_name ) - if checkit2(domains_in_query_seq, target_domain_names, target_domains, target_domain_architecure) + if checkit2(domains_in_query_seq, target_domain_names, target_domains, in_msa, out_domain_msas, out_domain_architecture_msa, target_domain_architecure) passing_sequences.push(domains_in_query_seq) end domains_in_query_seq = Array.new @@ -138,11 +140,19 @@ module Evoruby if prev_query_seq_name != nil total_sequences += 1 - if checkit2(domains_in_query_seq, target_domain_names, target_domains, target_domain_architecure) + if checkit2(domains_in_query_seq, target_domain_names, target_domains, in_msa, out_domain_msas, out_domain_architecture_msa, target_domain_architecure) passing_sequences.push(domains_in_query_seq) end end + out_domain_msas.keys.sort.each do |domain_name| + puts "writing #{domain_name}" + write_msa( out_domain_msas[domain_name], domain_name + ".fasta" ) + end + + puts "writing target_domain_architecure" + write_msa( out_domain_architecture_msa, "target_domain_architecure" + ".fasta" ) + passing_sequences.each do | domains | seq = domains[0].query @@ -168,192 +178,9 @@ module Evoruby puts "total sequences : " + total_sequences.to_s puts "passing sequences: " + passing_sequences.size.to_s - #### - - 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 ) || ( length >= length_threshold.to_f ) ) ) - hmmscan_datas << HmmscanData.new( sequence, number, out_of, env_from, env_to, i_e_value ) - 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 = passing_domains_per_protein - 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_domain_number, - out_msa ) - 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 - 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 - 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 - - 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( "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_multi_seqs.get_number_of_seqs.to_s ) - #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 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 - - write_msa( out_msa, outfile + ".fasta" ) - write_msa( passed_multi_seqs, passed_seqs_outfile ) - write_msa( failed_seqs, failed_seqs_outfile ) + # write_msa( out_msa, outfile + ".fasta" ) + # write_msa( passed_multi_seqs, passed_seqs_outfile ) + # write_msa( failed_seqs, failed_seqs_outfile ) log << ld log << "passing target domains : " + domain_pass_counter.to_s + ld @@ -372,7 +199,18 @@ module Evoruby private - def checkit2(domains_in_query_seq, target_domain_names, target_domains, target_domain_architecture = nil) + # domains_in_query_seq: Array of HmmscanResult + # target_domain_names: Set of String + # target_domains: Hash String->TargetDomain + # target_domain_architecture: String + def checkit2(domains_in_query_seq, + target_domain_names, + target_domains, + in_msa, + out_domain_msas, + out_domain_architecture_msa, + target_domain_architecture = nil) + domain_names_in_query_seq = Set.new domains_in_query_seq.each do |domain| domain_names_in_query_seq.add(domain.model) @@ -380,6 +218,7 @@ module Evoruby if (target_domain_names.subset?(domain_names_in_query_seq)) passed_domains = Array.new + passed_domains_counts = Hash.new domains_in_query_seq.each do |domain| if target_domains.has_key?(domain.model) @@ -407,8 +246,14 @@ module Evoruby passed_domains.push(domain) end + if (passed_domains_counts.key?(domain.model)) + passed_domains_counts[domain.model] = passed_domains_counts[domain.model] + 1 + else + passed_domains_counts[domain.model] = 1 + end + if (@passed.key?(domain.model)) - @passed[domain.model] = @passed[domain.model] + 1 + @passed[domain.model] = @passed[domain.model] + 1 else @passed[domain.model] = 1 end @@ -418,17 +263,83 @@ module Evoruby else return false end + passed_domains.sort! { |a,b| a.ali_from <=> b.ali_from } # Compare architectures if target_domain_architecture != nil if !compareArchitectures(target_domain_architecture, passed_domains) return false end end + + domain_counter = Hash.new + + min_env_from = 10000000 + max_env_from = 0 + min_env_to = 10000000 + max_env_to = 0 + + query_seq = nil + + passed_domains.each do |domain| + domain_name = domain.model + + unless out_domain_msas.has_key? domain_name + out_domain_msas[ domain_name ] = Msa.new + end + + if domain_counter.key?(domain_name) + domain_counter[domain_name] = domain_counter[domain_name] + 1 + else + domain_counter[domain_name] = 1 + end + + if query_seq == nil + query_seq = domain.query + query_seq.freeze + elsif query_seq != domain.query + error_msg = "seq names do not match: this should not have happened" + raise StandardError, error_msg + end + + extract_domain( query_seq, + domain_counter[domain_name], + passed_domains_counts[domain_name], + domain.env_from, + domain.env_to, + in_msa, + out_domain_msas[ domain_name ] ) + + if domain.env_from < min_env_from + min_env_from = domain.env_from + end + if domain.env_from > max_env_from + max_env_from = domain.env_from + end + if domain.env_to < min_env_to + min_env_to = domain.env_to + end + if domain.env_to > max_env_to + max_env_to = domain.env_to + end + end + + puts "env from: #{min_env_from} - #{max_env_from}" + puts "env to : #{min_env_to} - #{max_env_to}" + + extract_domain( query_seq, + 1, + 1, + min_env_from, + max_env_to, + in_msa, + out_domain_architecture_msa ) + + puts passed_domains_counts true end - def compareArchitectures(target_domain_architecture, passed_domains) - passed_domains.sort! { |a,b| a.ali_from <=> b.ali_from } + # passed_domains needs to be sorted! + def compareArchitectures(target_domain_architecture, passed_domains, strict = false) domain_architecture = "" passed_domains.each do |domain| if domain_architecture.length > 0 @@ -436,7 +347,12 @@ module Evoruby end domain_architecture += domain.model end - pass = (target_domain_architecture == domain_architecture) + pass = false + if strict + pass = (target_domain_architecture == domain_architecture) + else + pass = (domain_architecture.index(target_domain_architecture) != nil) + end if !pass if (@non_passsing_domain_architectures.key?(domain_architecture)) @non_passsing_domain_architectures[domain_architecture] = @non_passsing_domain_architectures[domain_architecture] + 1 @@ -452,6 +368,7 @@ module Evoruby w = FastaWriter.new() w.set_line_width( 60 ) w.clean( true ) + File.delete(filename) if File.exist?(filename) #TODO remove me begin io.write_to_file( msa, filename, w ) rescue Exception @@ -474,50 +391,14 @@ module Evoruby add_to_msa.add_sequence( seq ) end - def process_hmmscan_datas( hmmscan_datas, - in_msa, - add_domain_number, - out_msa ) - - actual_out_of = hmmscan_datas.size - - 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_domain_number ) - - 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 - end # def process_hmmscan_data - - def extract_domain( sequence, + def extract_domain( seq_name, number, out_of, seq_from, seq_to, in_msa, - out_msa, - add_domain_number) - if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of ) + out_msa) + if 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 @@ -525,13 +406,13 @@ module Evoruby 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 ) + seqs = in_msa.find_by_name_start(seq_name, true) if seqs.length < 1 - error_msg = "sequence \"" + sequence + "\" not found in sequence file" + error_msg = "sequence \"" + seq_name + "\" not found in sequence file" raise IOError, error_msg end if seqs.length > 1 - error_msg = "sequence \"" + sequence + "\" not unique in sequence file" + error_msg = "sequence \"" + seq_name + "\" not unique in sequence file" raise IOError, error_msg end # hmmscan is 1 based, whereas sequences are 0 bases in this package. @@ -541,7 +422,7 @@ module Evoruby seq.set_name( orig_name.split[ 0 ] ) - if out_of != 1 && add_domain_number + if out_of != 1 seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s ) end @@ -554,18 +435,6 @@ module Evoruby end # class HmmscanDomainExtractor - class HmmscanData - 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 - class TargetDomain def initialize( name, i_e_value, abs_len, rel_len, position ) @name = name