From 8a4f118ddf875a7e7c17fbbd902116d5648ce805 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 5 Jan 2013 00:56:20 +0000 Subject: [PATCH] inprogress --- .../ruby/evoruby/lib/evo/tool/hmmscan_summary.rb | 42 ++++++++------------ 1 file changed, 16 insertions(+), 26 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb index 55ba7a4..3b29968 100644 --- a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb +++ b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb @@ -6,7 +6,6 @@ # # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $ # -# last modified: 121003 require 'set' @@ -21,12 +20,12 @@ module Evoruby class HmmscanSummary PRG_NAME = "hsp" - PRG_VERSION = "2.000" + PRG_VERSION = "2.001" PRG_DESC = "hmmscan summary" - PRG_DATE = "2012.10.23" - COPYRIGHT = "2012 Christian M Zmasek" - CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" + PRG_DATE = "2013.10.23" + 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" @@ -49,8 +48,6 @@ module Evoruby def run - - Util.print_program_information( PRG_NAME, PRG_VERSION, PRG_DESC, @@ -222,7 +219,6 @@ module Evoruby 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 + ")" ) @@ -248,8 +244,6 @@ module Evoruby uniprot, species ) - - Util.check_file_for_readability( inpath ) Util.check_file_for_writability( outpath ) @@ -267,8 +261,6 @@ module Evoruby hmmscan_results_per_protein = [] - - prev_query = "" results.each do | r | @@ -326,13 +318,12 @@ module Evoruby fs_e_value_threshold, hmm_for_protein_output, i_e_value_threshold, - false, + uniprot, species ) end outfile.flush() outfile.close() - end # def parse def process_id( id ) @@ -342,8 +333,6 @@ module Evoruby id end - - def count_model( model ) if ( @domain_counts.has_key?( model ) ) count = @domain_counts[ model ].to_i @@ -369,13 +358,12 @@ module Evoruby hmmscan_results_per_protein.each do | r | - if r.model == hmm_for_protein_output - if i_e_value_threshold >= 0.0 && r.fs_e_value > fs_e_value_threshold + if i_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold return end end - if i_e_value_threshold < 0 || 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 @@ -409,12 +397,14 @@ module Evoruby end s << "\t" - #e = UniprotKB::get_entry_by_id( process_id( own.query ) ) + if !uniprotkb.empty? + #e = UniprotKB::get_entry_by_id( process_id( own.query ) ) - #if e != nil - # s << uniprot_annotation( e ) - # # s << "\uniprot_annotationt" - #end + #if e != nil + # s << uniprot_annotation( e ) + # # s << "\uniprot_annotationt" + #end + end overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) @@ -509,7 +499,6 @@ module Evoruby end - def print_help() puts( "Usage:" ) puts() @@ -521,6 +510,7 @@ 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 -- 1.7.10.2