From 43c5c23c5626c0e28c21cb986d4ab0da0400973c Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 20 Jul 2012 21:22:16 +0000 Subject: [PATCH] linkers! --- .../ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb index ef709e9..7a8eb6e 100644 --- a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb @@ -106,7 +106,7 @@ module Evoruby end extract_linkers = false - if cla.is_option_set?(EXTRACT_LINKERS_OPTIO) + if cla.is_option_set?(EXTRACT_LINKERS_OPTION) extract_linkers = true end @@ -241,7 +241,7 @@ module Evoruby File.open( input_file ) do | file | while line = file.gets line.strip! - if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) + if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) values = line.split( PROTEINS_LIST_FILE_SEPARATOR ) mod_line = nil if ( values.length < 2 ) @@ -311,7 +311,7 @@ module Evoruby ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER ) orig_name = nil - if seq != nil + if seq != nil orig_name = seq.get_name seq.set_name( seq.get_name + " [" + current_species + "]" ) new_msa.add_sequence( seq ) @@ -382,7 +382,7 @@ module Evoruby if mod_line puts mod_line end - end # !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) + end # !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) end # while line = file.gets end @@ -523,10 +523,10 @@ module Evoruby "and possibly genome multiple-sequence ('fasta') files> [mapping file for " + "genome multiple-sequence ('fasta') files not in input dir]" ) puts() - puts( " option: -" + EXT_OPTION + "=: to extend extracted domains" ) + puts( " option: -" + EXT_OPTION + "=: to extend extracted domains" ) puts( " -" + EXTRACT_LINKERS_OPTION + " : to extract linkers" ) puts() - puts( " " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" ) + puts( " " + "Example: \"mse.rb .prot . protein_seqs domain_seqs ../genome_locations.txt\"" ) puts() end -- 1.7.10.2