From 89aee5121a1586788e45d9fc51827c5c6b148dca Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 01:08:45 +0000 Subject: [PATCH] in progress --- .../evoruby/lib/evo/apps/taxonomy_processor.rb | 22 +++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb index 5b41b2b..d316f85 100644 --- a/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb +++ b/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb @@ -22,10 +22,10 @@ module Evoruby class TaxonomyProcessor PRG_NAME = "tap" - PRG_DATE = "2010.02.24" + PRG_DATE = "2012.09.27" PRG_DESC = "replacement of species names in multiple sequence files" - PRG_VERSION = "1.01" - COPYRIGHT = "2010 Christian M Zmasek" + PRG_VERSION = "1.02" + COPYRIGHT = "2012 Christian M Zmasek" CONTACT = "phylosoft@gmail.com" WWW = "www.phylosoft.org" @@ -62,14 +62,14 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end - + mapfile = nil input = nil output = nil list_file = nil - - + + if cla.get_number_of_files == 4 mapfile = cla.get_file_name( 0 ) input = cla.get_file_name( 1 ) @@ -80,13 +80,15 @@ module Evoruby output = cla.get_file_name( 1 ) list_file = cla.get_file_name( 2 ) elsif cla.get_number_of_files == 1 - input = cla.get_file_name( 0 ) + input = cla.get_file_name( 0 ) i = nil if input.downcase.end_with?( ".fasta" ) - i = input[ 0 .. input.length - 6 ] + i = input[ 0 .. input.length - 7 ] + elsif input.downcase.end_with?( ".fsa" ) + i = input[ 0 .. input.length - 5 ] else i = input - end + end output = i + "_ni.fasta" list_file = i + ".nim" end @@ -212,7 +214,7 @@ module Evoruby def modify_name( desc, counter, file, species_map, extract_taxonomy ) new_desc = nil my_species = nil - # if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/ + # if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/ if desc =~ /^>?\s*\S{1,10}_([A-Z]{3,5})/ new_desc = counter.to_s( 16 ) + "_" + $1 elsif SIMPLE -- 1.7.10.2