From fd508ee418219eda297f3a4da5f4d3be7f8a6db8 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 22 Mar 2013 22:54:15 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb | 8 ++++---- forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb | 6 ++++-- forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb | 7 ++++--- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb index b499c72..5695cd4 100644 --- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb @@ -25,10 +25,10 @@ module Evoruby PRG_NAME = "mse" PRG_VERSION = "1.02" PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files" - PRG_DATE = "2012.07.20" - COPYRIGHT = "2008-2012 Christian M Zmasek" + PRG_DATE = "130322" + COPYRIGHT = "2008-2013 Christian M Zmasek" CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" + WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" HELP_OPTION_1 = 'help' HELP_OPTION_2 = 'h' @@ -314,7 +314,7 @@ module Evoruby per_species_counter.to_i - ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER ) + ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER ) orig_name = nil if seq != nil diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 1128be6..4e26acb 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -10,7 +10,7 @@ # $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $ # # Environment variable FORESTER_HOME needs to point to the appropriate -# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/) +# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/) require 'lib/evo/util/constants' require 'lib/evo/util/util' @@ -44,7 +44,7 @@ module Evoruby PRG_VERSION = "1.02" COPYRIGHT = "2012 Christian M Zmasek" CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" + WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" IDS_ONLY_OPTION = "n" DOMAINS_ONLY_OPTION = "d" @@ -224,6 +224,7 @@ module Evoruby cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + '-f=d ' + phylogeny_file + ' ' + domains_mapfile_name + ' ' + my_outfile + puts cmd execute_cmd( cmd, log ) end @@ -236,6 +237,7 @@ module Evoruby cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + '-f=n ' + my_infile + ' ' + ids_mapfile_name + ' ' + outfile + puts cmd execute_cmd( cmd, log ) end diff --git a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb index 8496d36..9a77601 100644 --- a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb @@ -22,9 +22,9 @@ module Evoruby class TaxonomyProcessor PRG_NAME = "tap" - PRG_DATE = "2013.03.20" + PRG_DATE = "2013.03.22" PRG_DESC = "replacement of species names in multiple sequence files" - PRG_VERSION = "2.00" + PRG_VERSION = "2.001" COPYRIGHT = "2013 Christian M Zmasek" CONTACT = "phylosoft@gmail.com" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" @@ -167,6 +167,7 @@ module Evoruby def modify_name( desc, counter, file, extract_taxonomy ) new_desc = nil + desc.gsub!( /\s+/, ' ' ) if desc =~ /^>?\s*\S{1,10}_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)/ new_desc = counter.to_s( 16 ) + "_" + $1 elsif extract_taxonomy @@ -178,7 +179,7 @@ module Evoruby else new_desc = counter.to_s( 16 ) end - file.print( new_desc + ": " + desc + "\n" ) + file.print( new_desc + "\t" + desc + "\n" ) new_desc end -- 1.7.10.2