X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fhmmscan_summary.rb;h=913be50caff607df33d51f9088dc1e2b7d3879fa;hb=c601ea93eccd96596109723253ca77a70b7e94b5;hp=9c5e3a99637f7ec4759e27638356df8205e0f748;hpb=79fbb03cb44e42992dcb01f0f64386d59c243838;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 9c5e3a9..913be50 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -1,17 +1,20 @@ # -# = lib/evo/apps/hmmscan_parser.rb - HmmscanParser class +# = lib/evo/tool/hmmscan_summary.rb - HmmscanSummary class # -# Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek +# Copyright:: Copyright (C) 2012 Christian M. Zmasek # License:: GNU Lesser General Public License (LGPL) # # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $ # -# last modified: 11/24/2009 +# last modified: 121003 + +require 'set' 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 @@ -19,18 +22,20 @@ module Evoruby PRG_NAME = "hsp" PRG_VERSION = "2.000" - PRG_DESC = "hmmscan parser" - PRG_DATE = "2012.10.19" + PRG_DESC = "hmmscan summary" + PRG_DATE = "2012.10.23" COPYRIGHT = "2012 Christian M Zmasek" CONTACT = "phylosoft@gmail.com" WWW = "www.phylosoft.org" DELIMITER_OPTION = "d" + SPECIES_OPTION = "s" I_E_VALUE_THRESHOLD_OPTION = "ie" FS_E_VALUE_THRESHOLD_OPTION = "pe" HMM_FOR_PROTEIN_OUTPUT = "m" IGNORE_DUF_OPTION = "i" PARSE_OUT_DESCRIPITION_OPTION = "a" + UNIPROT = "u" HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" @@ -44,6 +49,8 @@ module Evoruby def run + + Util.print_program_information( PRG_NAME, PRG_VERSION, PRG_DESC, @@ -60,7 +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 @@ -77,6 +84,8 @@ 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 ) if ( disallowed.length > 0 ) @@ -109,6 +118,8 @@ module Evoruby end end + + fs_e_value_threshold = -1.0 if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) ) begin @@ -130,6 +141,24 @@ 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 + species = cla.get_option_value( SPECIES_OPTION ) + rescue ArgumentError => e + Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT ) + end + end + ignore_dufs = false if ( cla.is_option_set?( IGNORE_DUF_OPTION ) ) ignore_dufs = true @@ -143,6 +172,7 @@ module Evoruby 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 @@ -163,14 +193,17 @@ module Evoruby else puts( "column delimiter : " + column_delimiter ) end - if ( fs_e_value_threshold >= 0.0 ) + 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? ) + if !hmm_for_protein_output.empty? puts( "HMM for proteins : " + hmm_for_protein_output ) end + if !uniprot.empty? + puts( "Uniprot : " + uniprot ) + end puts() begin @@ -181,8 +214,10 @@ module Evoruby ignore_dufs, parse_descriptions, fs_e_value_threshold, - hmm_for_protein_output ) - rescue ArgumentError, IOError => e + 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() @@ -209,10 +244,18 @@ module Evoruby ignore_dufs, get_descriptions, fs_e_value_threshold, - hmm_for_protein_output ) + hmm_for_protein_output, + uniprot, + species ) + + + Util.check_file_for_readability( inpath ) Util.check_file_for_writability( outpath ) + hmmscan_parser = HmmscanParser.new( inpath ) + results = hmmscan_parser.parse + outfile = File.open( outpath, "a" ) query = "" @@ -224,11 +267,11 @@ module Evoruby hmmscan_results_per_protein = [] - hmmscan_parser = HmmscanParser.new( inpath ) + prev_query = "" - hmmscan_parser.parse.each do | r | + results.each do | r | model = r.model query = r.query i_e_value = r.i_e_value @@ -236,21 +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 @@ -260,7 +303,8 @@ module Evoruby process_hmmscan_results_per_protein( hmmscan_results_per_protein, fs_e_value_threshold, hmm_for_protein_output, - i_e_value_threshold ) + i_e_value_threshold, + true ) end hmmscan_results_per_protein.clear end @@ -275,19 +319,28 @@ module Evoruby 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 + if !hmm_for_protein_output.empty? && !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, + true ) end + outfile.flush() outfile.close() end # def parse + def process_id( id ) + if id =~ /(sp|tr)\|\S+\|(\S+)/ + id = $2 + end + id + end + + + def count_model( model ) if ( @domain_counts.has_key?( model ) ) count = @domain_counts[ model ].to_i @@ -301,7 +354,8 @@ module Evoruby def process_hmmscan_results_per_protein( hmmscan_results_per_protein, fs_e_value_threshold, hmm_for_protein_output, - i_e_value_threshold ) + i_e_value_threshold, + uniprotkb ) dc = 0 # filter according to i-Evalue threshold @@ -338,7 +392,7 @@ module Evoruby s = "" s << own.query + "\t" - s << "HUMAN" + "\t" + s << species + "\t" s << own.fs_e_value.to_s + "\t" s << own.qlen.to_s + "\t" s << dc.to_s + "\t" @@ -347,10 +401,16 @@ module Evoruby s << r.model + " " end s << "\t" + e = UniprotKB::get_entry_by_id( process_id( own.query ) ) + + if e != nil + s << uniprot_annotation( e ) + s << "\uniprot_annotationt" + end overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) - s << overview + "\t" + s << overview + "\t" s << calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + "\t" @@ -374,6 +434,18 @@ module Evoruby 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 = ""