X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fhmmscan_summary.rb;h=08de9c125e9385c009c34134d8a87d8e4cf90f0e;hb=156517428746b21481eb815bf860ffb6cb0314ef;hp=bb32da53ffc2b38470d5347f45c2ea97ca9d5935;hpb=82e8764c422ba00b61bf62496d2c7b409a088a20;p=jalview.git diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb index bb32da5..08de9c1 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -13,16 +13,15 @@ require 'lib/evo/util/constants' require 'lib/evo/util/util' require 'lib/evo/util/command_line_arguments' require 'lib/evo/io/parser/hmmscan_parser' -require 'lib/evo/io/web/uniprotkb' module Evoruby class HmmscanSummary PRG_NAME = "hsp" - PRG_VERSION = "2.001" + PRG_VERSION = "2.002" PRG_DESC = "hmmscan summary" - PRG_DATE = "2013.10.23" + PRG_DATE = "130319" COPYRIGHT = "2013 Christian M Zmasek" CONTACT = "phyloxml@gmail.com" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" @@ -34,7 +33,6 @@ module Evoruby HMM_FOR_PROTEIN_OUTPUT = "m" IGNORE_DUF_OPTION = "i" PARSE_OUT_DESCRIPITION_OPTION = "a" - UNIPROT = "u" HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" @@ -48,14 +46,14 @@ module Evoruby def run - # Util.print_program_information( PRG_NAME, - # PRG_VERSION, - # PRG_DESC, - # PRG_DATE, - # COPYRIGHT, - # CONTACT, - # WWW, - # STDOUT ) + Util.print_program_information( PRG_NAME, + PRG_VERSION, + PRG_DESC, + PRG_DATE, + COPYRIGHT, + CONTACT, + WWW, + STDOUT ) begin cla = CommandLineArguments.new( ARGV ) @@ -81,7 +79,6 @@ module Evoruby allowed_opts.push( IGNORE_DUF_OPTION ) allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION ) allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT ) - allowed_opts.push( UNIPROT ) allowed_opts.push( SPECIES_OPTION ) disallowed = cla.validate_allowed_options_as_str( allowed_opts ) @@ -115,8 +112,6 @@ module Evoruby end end - - fs_e_value_threshold = -1.0 if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) ) begin @@ -138,15 +133,6 @@ module Evoruby end end - uniprot = "" - if ( cla.is_option_set?( UNIPROT ) ) - begin - uniprot = cla.get_option_value( UNIPROT ) - rescue ArgumentError => e - Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT ) - end - end - species = "HUMAN" if ( cla.is_option_set?( SPECIES_OPTION ) ) begin @@ -166,42 +152,39 @@ module Evoruby parse_descriptions = true end -# puts() -# puts( "hmmpfam outputfile : " + inpath ) -# puts( "outputfile : " + outpath ) -# puts( "species : " + species ) -# if ( i_e_value_threshold >= 0.0 ) -# puts( "i-E-value threshold : " + i_e_value_threshold.to_s ) -# else -# puts( "i-E-value threshold : no threshold" ) -# end -# if ( parse_descriptions ) -# puts( "parse descriptions : true" ) -# else -# puts( "parse descriptions : false" ) -# end -# if ( ignore_dufs ) -# puts( "ignore DUFs : true" ) -# else -# puts( "ignore DUFs : false" ) -# end -# if ( column_delimiter == "\t" ) -# puts( "column delimiter : TAB" ) -# else -# puts( "column delimiter : " + column_delimiter ) -# end -# if fs_e_value_threshold >= 0.0 -# puts( "E-value threshold : " + fs_e_value_threshold.to_s ) -# else -# puts( "E-value threshold : no threshold" ) -# end -# if !hmm_for_protein_output.empty? -# puts( "HMM for proteins : " + hmm_for_protein_output ) -# end -# if !uniprot.empty? -# puts( "Uniprot : " + uniprot ) -# end -# puts() + puts() + puts( "hmmpfam outputfile : " + inpath ) + puts( "outputfile : " + outpath ) + puts( "species : " + species ) + if ( i_e_value_threshold >= 0.0 ) + puts( "i-E-value threshold : " + i_e_value_threshold.to_s ) + else + puts( "i-E-value threshold : no threshold" ) + end + if ( parse_descriptions ) + puts( "parse descriptions : true" ) + else + puts( "parse descriptions : false" ) + end + if ( ignore_dufs ) + puts( "ignore DUFs : true" ) + else + puts( "ignore DUFs : false" ) + end + if ( column_delimiter == "\t" ) + puts( "column delimiter : TAB" ) + else + puts( "column delimiter : " + column_delimiter ) + end + if fs_e_value_threshold >= 0.0 + puts( "E-value threshold : " + fs_e_value_threshold.to_s ) + else + puts( "E-value threshold : no threshold" ) + end + if !hmm_for_protein_output.empty? + puts( "HMM for proteins : " + hmm_for_protein_output ) + end + puts() begin parse( inpath, @@ -212,21 +195,20 @@ module Evoruby parse_descriptions, fs_e_value_threshold, hmm_for_protein_output, - uniprot, species ) rescue IOError => e Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT ) end domain_counts = get_domain_counts() -# puts -# puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" ) -# puts( "(number of different domains: " + domain_counts.length.to_s + ")" ) -# puts -# puts( Util.draw_histogram( domain_counts, "#" ) ) -# puts -# Util.print_message( PRG_NAME, 'OK' ) -# puts + puts + puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" ) + puts( "(number of different domains: " + domain_counts.length.to_s + ")" ) + puts + puts( Util.draw_histogram( domain_counts, "#" ) ) + puts + Util.print_message( PRG_NAME, 'OK' ) + puts end # def run @@ -241,7 +223,6 @@ module Evoruby get_descriptions, fs_e_value_threshold, hmm_for_protein_output, - uniprot, species ) Util.check_file_for_readability( inpath ) @@ -296,7 +277,6 @@ module Evoruby fs_e_value_threshold, hmm_for_protein_output, i_e_value_threshold, - uniprot, species ) end hmmscan_results_per_protein.clear @@ -318,7 +298,6 @@ module Evoruby fs_e_value_threshold, hmm_for_protein_output, i_e_value_threshold, - uniprot, species ) end @@ -347,7 +326,6 @@ module Evoruby fs_e_value_threshold, hmm_for_protein_output, i_e_value_threshold, - uniprotkb, species ) dc = 0 @@ -397,15 +375,6 @@ module Evoruby end s << "\t" - if !uniprotkb.empty? - #e = UniprotKB::get_entry_by_id( process_id( own.query ) ) - - #if e != nil - # s << uniprot_annotation( e ) - # # s << "\uniprot_annotationt" - #end - end - overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) s << overview + "\t" @@ -414,7 +383,6 @@ module Evoruby 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 @@ -428,23 +396,10 @@ module Evoruby s << "]" prev_r = r end - s << make_interdomain_sequence( own.qlen - prev_r.env_from, false ) + s << make_interdomain_sequence( own.qlen - prev_r.env_to, false ) puts s end - def uniprot_annotation( e ) - s = "" - pdb_ids = e.get_pdb_ids - if !pdb_ids.empty? - pdb_ids.each do | pdb | - s << pdb << ", " - end - else - s << "-" - end - s - end - def calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) linkers = "" prev_r = nil