X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fmulti_sequence_extractor.rb;h=77935cde14100c176b613a2f55794e02b1dc7043;hb=968e6e38c05f4add3ec8c51518285a03aadb7d5e;hp=0c525adf94bf1314eab522719b766c1381f4df64;hpb=de48eb9258a47840a28da964676707f659846ea2;p=jalview.git 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 0c525ad..77935cd 100644 --- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb @@ -1,10 +1,9 @@ # # = lib/evo/apps/multi_sequence_extractor.rb - MultiSequenceExtractor class # -# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek +# Copyright:: Copyright (C) 2014 Christian M. Zmasek # License:: GNU Lesser General Public License (LGPL) # -# $Id: multi_sequence_extractor.rb,v 1.10 2010/12/13 19:00:11 cmzmasek Exp $ require 'lib/evo/util/constants' @@ -16,18 +15,16 @@ require 'lib/evo/io/parser/fasta_parser' require 'lib/evo/io/writer/fasta_writer' require 'lib/evo/util/command_line_arguments' - - module Evoruby class MultiSequenceExtractor PRG_NAME = "mse" - PRG_VERSION = "1.03" + PRG_VERSION = "1.04" PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files" - PRG_DATE = "131127" - COPYRIGHT = "2008-2013 Christian M Zmasek" - CONTACT = "phylosoft@gmail.com" + PRG_DATE = "140318" + COPYRIGHT = "2014 Christian M Zmasek" + CONTACT = "phyloxml@gmail.com" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" HELP_OPTION_1 = 'help' HELP_OPTION_2 = 'h' @@ -71,7 +68,7 @@ module Evoruby exit( 0 ) end - if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 ) + if ( cla.get_number_of_files != 5 ) print_help exit( -1 ) end @@ -91,15 +88,12 @@ module Evoruby input_dir = cla.get_file_name( 1 ) out_dir = cla.get_file_name( 2 ) out_dir_doms = cla.get_file_name( 3 ) - mapping_file = nil + mapping_file = cla.get_file_name( 4 ) - if ( cla.get_number_of_files == 5 ) - mapping_file = cla.get_file_name( 4 ) - begin - Util.check_file_for_readability( mapping_file ) - rescue ArgumentError => e - Util.fatal_error( PRG_NAME, "error: " + e.to_s ) - end + begin + Util.check_file_for_readability( mapping_file ) + rescue ArgumentError => e + Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end extension = 0 @@ -115,26 +109,32 @@ module Evoruby extract_linkers = true end - if !File.exist?( input_dir ) + unless File.exist?( out_dir ) + Dir.mkdir( out_dir ) + end + unless File.exist?( out_dir_doms ) + Dir.mkdir( out_dir_doms ) + end + + unless File.exist?( input_dir ) Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" ) end - if !File.exist?( out_dir ) + unless File.exist?( out_dir ) Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" ) end - if !File.exist?( out_dir_doms ) + unless File.exist?( out_dir_doms ) Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" ) end - if !File.directory?( input_dir ) + unless File.directory?( input_dir ) Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" ) end - if !File.directory?( out_dir ) + unless File.directory?( out_dir ) Util.fatal_error( PRG_NAME, "error: [#{out_dir}] is not a directory" ) end - if !File.directory?( out_dir_doms ) + unless File.directory?( out_dir_doms ) Util.fatal_error( PRG_NAME, "error: [#{out_dir_doms}] is not a directory" ) end - log = String.new log << "Program : " + PRG_NAME + ld @@ -150,10 +150,8 @@ module Evoruby log << "Output dir : " + out_dir + ld puts( "Output dir domains : " + out_dir_doms ) log << "Output dir domains : " + out_dir_doms + ld - if ( mapping_file != nil ) - puts( "Mapping file : " + mapping_file ) - log << "Mapping file : " + mapping_file + ld - end + puts( "Mapping file : " + mapping_file ) + log << "Mapping file : " + mapping_file + ld if extension > 0 puts( "Extension : " + extension.to_s ) log << "Extension : " + extension.to_s + ld @@ -165,9 +163,7 @@ module Evoruby log << "Date : " + Time.now.to_s + ld puts - if ( mapping_file != nil ) - species_codes_to_paths = extract_mappings( mapping_file ) - end + species_codes_to_paths = extract_mappings( mapping_file ) input_files = obtain_inputfiles( input_dir, seq_names_files_suffix ) @@ -326,7 +322,7 @@ module Evoruby seq.set_name( seq.get_name + " [" + current_species + "]" ) new_msa.add_sequence( seq ) else - Util.fatal_error( PRG_NAME, "unexected error: seq is nil" ) + Util.fatal_error( PRG_NAME, "unexpected error: seq is nil" ) end if domain_ranges != nil @@ -495,19 +491,19 @@ module Evoruby if ( species_code_to_path.has_value?( path ) ) Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" ) end - if ( !File.exist?( path ) ) + unless ( File.exist?( path ) ) Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" ) end - if ( !File.file?( path ) ) + unless ( File.file?( path ) ) Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" ) end - if ( !File.readable?( path ) ) + unless ( File.readable?( path ) ) Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" ) end - if ( File.size( path ) < 10000 ) + if ( File.size( path ) < 1000 ) Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" ) end - if ( !Util.looks_like_fasta?( path ) ) + unless ( Util.looks_like_fasta?( path ) ) Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" ) end species_code_to_path[ species ] = path @@ -547,9 +543,8 @@ module Evoruby def print_help() puts( "Usage:" ) puts() - puts( " " + PRG_NAME + ".rb [mapping file for " + - "genome multiple-sequence ('fasta') files not in input dir]" ) + puts( " " + PRG_NAME + ".rb " + + " " ) puts() puts( " option: -" + EXT_OPTION + "=: to extend extracted domains" ) puts( " -" + EXTRACT_LINKERS_OPTION + " : to extract linkers" )