From: cmzmasek@gmail.com Date: Sat, 5 Jan 2013 00:43:44 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=792c99a676c550ba5de1e4d215c765bc75408a4b;p=jalview.git inprogress --- diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb index 3a9d662..55ba7a4 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -67,7 +67,7 @@ module Evoruby end if ( cla.is_option_set?( HELP_OPTION_1 ) || - cla.is_option_set?( HELP_OPTION_2 ) ) + cla.is_option_set?( HELP_OPTION_2 ) ) print_help exit( 0 ) end @@ -118,7 +118,7 @@ module Evoruby end end - + fs_e_value_threshold = -1.0 if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) ) @@ -151,7 +151,7 @@ module Evoruby end species = "HUMAN" - if ( cla.is_option_set?( SPECIES_OPTION ) ) + if ( cla.is_option_set?( SPECIES_OPTION ) ) begin species = cla.get_option_value( SPECIES_OPTION ) rescue ArgumentError => e @@ -279,21 +279,21 @@ module Evoruby env_to = r.env_to if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) && - ( !ignore_dufs || ( model !~ /^DUF\d+/ ) ) + ( !ignore_dufs || ( model !~ /^DUF\d+/ ) ) count_model( model ) outfile.print( query + - column_delimiter ) + column_delimiter ) if ( get_descriptions ) outfile.print( desc + - column_delimiter ) + 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 ) + 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 @@ -320,7 +320,7 @@ module Evoruby end end end - + if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty? process_hmmscan_results_per_protein( hmmscan_results_per_protein, fs_e_value_threshold, @@ -359,9 +359,7 @@ module Evoruby hmm_for_protein_output, i_e_value_threshold, uniprotkb, - species ) - - + species ) dc = 0 # filter according to i-Evalue threshold @@ -369,11 +367,9 @@ module Evoruby hmmscan_results_per_protein_filtered = [] hmmscan_results_per_protein.each do | r | - - puts r.model - puts r.fs_e_value - puts fs_e_value_threshold - + + + if r.model == hmm_for_protein_output if i_e_value_threshold >= 0.0 && r.fs_e_value > fs_e_value_threshold return @@ -412,7 +408,7 @@ module Evoruby s << r.model + " " end s << "\t" - puts s + #e = UniprotKB::get_entry_by_id( process_id( own.query ) ) #if e != nil