X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fhmmscan_summary.rb;h=08de9c125e9385c009c34134d8a87d8e4cf90f0e;hb=7e37741c149bbf6c27555ab9cf92766155d3f4d3;hp=82b27823333a20b07a1c0747639484c5e29746da;hpb=fea8aa1f2d8d2eebfbbb57ede28edc003367c12f;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 82b2782..08de9c1 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -6,33 +6,33 @@ # # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $ # -# 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/parser/uniprot_parser' module Evoruby class HmmscanSummary PRG_NAME = "hsp" - PRG_VERSION = "2.000" + PRG_VERSION = "2.002" PRG_DESC = "hmmscan summary" - PRG_DATE = "2012.10.19" - COPYRIGHT = "2012 Christian M Zmasek" - CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" + PRG_DATE = "130319" + COPYRIGHT = "2013 Christian M Zmasek" + CONTACT = "phyloxml@gmail.com" + WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" 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" @@ -79,7 +79,7 @@ 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 ) @@ -132,11 +132,11 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT ) end end - - uniprot = "" - if ( cla.is_option_set?( UNIPROT ) ) + + species = "HUMAN" + if ( cla.is_option_set?( SPECIES_OPTION ) ) begin - uniprot = cla.get_option_value( UNIPROT ) + species = cla.get_option_value( SPECIES_OPTION ) rescue ArgumentError => e Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT ) end @@ -155,6 +155,7 @@ 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 @@ -175,17 +176,14 @@ 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 @@ -197,13 +195,12 @@ module Evoruby parse_descriptions, fs_e_value_threshold, hmm_for_protein_output, - uniprot ) - rescue ArgumentError, IOError => e + 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 + ")" ) @@ -226,18 +223,14 @@ module Evoruby get_descriptions, fs_e_value_threshold, 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 - - uniprot_entries = nil - if !uniprot.empty? - uniprot_entries = read_uniprot( results, uniprot ) - end - + outfile = File.open( outpath, "a" ) query = "" @@ -249,8 +242,6 @@ module Evoruby hmmscan_results_per_protein = [] - - prev_query = "" results.each do | r | @@ -285,7 +276,8 @@ 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, + species ) end hmmscan_results_per_protein.clear end @@ -300,30 +292,26 @@ 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, + species ) end + outfile.flush() outfile.close() - end # def parse - - def read_uniprot( hmmscan_results, uniprot ) - ids = [] - hmmscan_results.each do | r | - ids << r.query - end - uniprot_parser = UniprotParser.new uniprot - uniprot_entries = uniprot_parser.parse ids - uniprot_entries + 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 @@ -337,7 +325,8 @@ 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, + species ) dc = 0 # filter according to i-Evalue threshold @@ -345,12 +334,14 @@ module Evoruby 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 + if fs_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold return end end - if r.i_e_value <= i_e_value_threshold + if i_e_value_threshold <= 0 || r.i_e_value <= i_e_value_threshold hmmscan_results_per_protein_filtered << r if r.model == hmm_for_protein_output dc += 1 @@ -374,7 +365,7 @@ 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" @@ -386,13 +377,12 @@ module Evoruby 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" 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 @@ -406,11 +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 calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) linkers = "" prev_r = nil @@ -465,7 +454,6 @@ module Evoruby end - def print_help() puts( "Usage:" ) puts() @@ -477,6 +465,7 @@ module Evoruby puts( " -" + IGNORE_DUF_OPTION + ": ignore DUFs" ) puts( " -" + FS_E_VALUE_THRESHOLD_OPTION + ": E-value threshold for full protein sequences, only for protein summary" ) puts( " -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" ) + puts( " -" + SPECIES_OPTION + ": species for protein summary" ) puts() end