From 79fbb03cb44e42992dcb01f0f64386d59c243838 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 20 Oct 2012 02:52:50 +0000 Subject: [PATCH] in progress --- .../ruby/evoruby/lib/evo/tool/hmmscan_summary.rb | 362 +++++++++++++------- 1 file changed, 239 insertions(+), 123 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb index bb697b0..9c5e3a9 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -26,7 +26,7 @@ module Evoruby WWW = "www.phylosoft.org" DELIMITER_OPTION = "d" - I_E_VALUE_THRESHOLD_OPTION = "e" + I_E_VALUE_THRESHOLD_OPTION = "ie" FS_E_VALUE_THRESHOLD_OPTION = "pe" HMM_FOR_PROTEIN_OUTPUT = "m" IGNORE_DUF_OPTION = "i" @@ -34,128 +34,15 @@ module Evoruby HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" + USE_AVOID_HMMS = true + AVOID_HHMS = [ "RRM_1", "RRM_2", "RRM_3", "RRM_4", "RRM_5", "RRM_6" ] + LIMIT_FOR_CLOSE_DOMAINS = 20 + def initialize @domain_counts = Hash.new end - # raises ArgumentError, IOError - def parse( inpath, - outpath, - column_delimiter, - i_e_value_threshold, - ignore_dufs, - get_descriptions, - fs_e_value_threshold, - hmm_for_protein_output ) - Util.check_file_for_readability( inpath ) - Util.check_file_for_writability( outpath ) - - outfile = File.open( outpath, "a" ) - - query = "" - desc = "" - model = "" - env_from = "" - env_to = "" - i_e_value = "" - - hmmscan_results_per_protein = [] - - hmmscan_parser = HmmscanParser.new( inpath ) - - prev_query = "" - - hmmscan_parser.parse.each do | r | - model = r.model - query = r.query - i_e_value = r.i_e_value - env_from = r.env_from - env_to = r.env_to - - if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) && - ( !ignore_dufs || ( model !~ /^DUF\d+/ ) ) - count_model( model ) - outfile.print( query + - column_delimiter ) - if ( get_descriptions ) - outfile.print( desc + - column_delimiter ) - end - outfile.print( model + - column_delimiter + - env_from.to_s + - column_delimiter + - env_to.to_s + - column_delimiter + - i_e_value.to_s ) - outfile.print( Constants::LINE_DELIMITER ) - end - - if !prev_query.empty? && prev_query != query - if !hmmscan_results_per_protein.empty? - process_hmmscan_results_per_protein( hmmscan_results_per_protein, - fs_e_value_threshold, - hmm_for_protein_output ) - end - hmmscan_results_per_protein.clear - end - prev_query = query - hmmscan_results_per_protein << r - end - if !hmmscan_results_per_protein.empty? - process_hmmscan_results_per_protein( hmmscan_results_per_protein, - fs_e_value_threshold, - hmm_for_protein_output ) - end - outfile.flush() - outfile.close() - - end # def parse - - def count_model( model ) - if ( @domain_counts.has_key?( model ) ) - count = @domain_counts[ model ].to_i - count += 1 - @domain_counts[ model ] = count - else - @domain_counts[ model ] = 1 - end - end - - def process_hmmscan_results_per_protein( hmmscan_results_per_protein, - fs_e_value_threshold, - hmm_for_protein_output ) - - fs_e_value = -1 - hmmscan_results_per_protein.each do | r | - if r.model == hmm_for_protein_output - fs_e_value = r.fs_e_value - if fs_e_value > fs_e_value_threshold - return - end - end - end - - - first = hmmscan_results_per_protein[ 0 ] - s = "" - s << first.query + "\t" - s << fs_e_value.to_s + "\t" - s << first.qlen.to_s + "\t" - # s << first.fs_e_value.to_s + "\t" - # s << first.out_of.to_s + "\t" - hmmscan_results_per_protein.each do | r | - s << r.model + "|" - end - puts s - end - - - def get_domain_counts() - return @domain_counts - end - - def run() + def run Util.print_program_information( PRG_NAME, PRG_VERSION, @@ -234,7 +121,6 @@ module Evoruby end end - hmm_for_protein_output = "" if ( cla.is_option_set?( HMM_FOR_PROTEIN_OUTPUT ) ) begin @@ -244,7 +130,6 @@ module Evoruby end end - ignore_dufs = false if ( cla.is_option_set?( IGNORE_DUF_OPTION ) ) ignore_dufs = true @@ -312,7 +197,238 @@ module Evoruby Util.print_message( PRG_NAME, 'OK' ) puts - end # def run() + end # def run + + private + + # raises ArgumentError, IOError + def parse( inpath, + outpath, + column_delimiter, + i_e_value_threshold, + ignore_dufs, + get_descriptions, + fs_e_value_threshold, + hmm_for_protein_output ) + Util.check_file_for_readability( inpath ) + Util.check_file_for_writability( outpath ) + + outfile = File.open( outpath, "a" ) + + query = "" + desc = "" + model = "" + env_from = "" + env_to = "" + i_e_value = "" + + hmmscan_results_per_protein = [] + + hmmscan_parser = HmmscanParser.new( inpath ) + + prev_query = "" + + hmmscan_parser.parse.each do | r | + model = r.model + query = r.query + i_e_value = r.i_e_value + env_from = r.env_from + env_to = r.env_to + + if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) && + ( !ignore_dufs || ( model !~ /^DUF\d+/ ) ) + count_model( model ) + outfile.print( query + + column_delimiter ) + if ( get_descriptions ) + outfile.print( desc + + column_delimiter ) + end + outfile.print( model + + column_delimiter + + env_from.to_s + + column_delimiter + + env_to.to_s + + column_delimiter + + i_e_value.to_s ) + outfile.print( Constants::LINE_DELIMITER ) + end + + if !hmm_for_protein_output.empty? + if !prev_query.empty? && prev_query != query + if !hmmscan_results_per_protein.empty? + process_hmmscan_results_per_protein( hmmscan_results_per_protein, + fs_e_value_threshold, + hmm_for_protein_output, + i_e_value_threshold ) + end + hmmscan_results_per_protein.clear + end + prev_query = query + + if USE_AVOID_HMMS + if !AVOID_HHMS.include? r.model + hmmscan_results_per_protein << r + end + else + hmmscan_results_per_protein << r + end + end + end + if !hmm_for_protein_output.empty? + if !hmmscan_results_per_protein.empty? + process_hmmscan_results_per_protein( hmmscan_results_per_protein, + fs_e_value_threshold, + hmm_for_protein_output, + i_e_value_threshold ) + end + end + outfile.flush() + outfile.close() + + end # def parse + + def count_model( model ) + if ( @domain_counts.has_key?( model ) ) + count = @domain_counts[ model ].to_i + count += 1 + @domain_counts[ model ] = count + else + @domain_counts[ model ] = 1 + end + end + + def process_hmmscan_results_per_protein( hmmscan_results_per_protein, + fs_e_value_threshold, + hmm_for_protein_output, + i_e_value_threshold ) + + dc = 0 + # filter according to i-Evalue threshold + # abort if fs Evalue too high + hmmscan_results_per_protein_filtered = [] + + hmmscan_results_per_protein.each do | r | + if r.model == hmm_for_protein_output + if r.fs_e_value > fs_e_value_threshold + return + end + end + if r.i_e_value <= i_e_value_threshold + hmmscan_results_per_protein_filtered << r + if r.model == hmm_for_protein_output + dc += 1 + end + end + end + + if dc == 0 + # passed on protein E-value, failed in per domain E-values + return + end + + hmmscan_results_per_protein_filtered.sort! { |r1,r2| r1.env_from <=> r2.env_from } + + own = nil + hmmscan_results_per_protein_filtered.each do | r | + if r.model == hmm_for_protein_output + own = r + end + end + + s = "" + s << own.query + "\t" + s << "HUMAN" + "\t" + s << own.fs_e_value.to_s + "\t" + s << own.qlen.to_s + "\t" + s << dc.to_s + "\t" + s << hmmscan_results_per_protein_filtered.length.to_s + "\t" + hmmscan_results_per_protein_filtered.each do | r | + s << r.model + " " + end + s << "\t" + + overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + + s << overview + "\t" + + s << calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + "\t" + + prev_r = nil + hmmscan_results_per_protein_filtered.each do | r | + + if prev_r != nil + s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 ) + else + s << make_interdomain_sequence( r.env_from, false ) + end + s << r.model + s << "[" + s << r.env_from.to_s << "-" << r.env_to.to_s + s << "|ie=" << r.i_e_value.to_s + s << "|ce=" << r.c_e_value.to_s + s << "]" + prev_r = r + end + s << make_interdomain_sequence( own.qlen - prev_r.env_from, false ) + puts s + end + + + def calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + linkers = "" + prev_r = nil + hmmscan_results_per_protein_filtered.each do | r | + if r.model == hmm_for_protein_output + if prev_r != nil + linkers << ( r.env_from - prev_r.env_to - 1 ).to_s + " " + end + prev_r = r + end + end + linkers + end + + def get_domain_counts() + return @domain_counts + end + + def make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + overview = "" + prev_r = nil + hmmscan_results_per_protein_filtered.each do | r | + if r.model == hmm_for_protein_output + if prev_r == nil + overview << hmm_for_protein_output + else + if ( r.env_from - prev_r.env_to - 1 ) <= LIMIT_FOR_CLOSE_DOMAINS + overview << "~" << hmm_for_protein_output + else + overview << "----" << hmm_for_protein_output + end + end + prev_r = r + end + end + overview + end + + def make_interdomain_sequence( d, mark_short = true ) + s = "" + d /= 20 + if d >= 10 + s << "----//----" + elsif d >= 1 + d.times do + s << "-" + end + elsif mark_short + s << "~" + end + s + end + + def print_help() puts( "Usage:" ) @@ -328,6 +444,6 @@ module Evoruby puts() end - end # class HmmscanParser + end # class end # module Evoruby \ No newline at end of file -- 1.7.10.2