From: zma Date: Tue, 14 Feb 2017 18:10:12 +0000 (-0800) Subject: removed X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6286ef87daebd189a0dcd7fc65f8f54c8ed126f6;p=jalview.git removed --- diff --git a/forester/ruby/evoruby/lib/evo/tool/new_tap.rb b/forester/ruby/evoruby/lib/evo/tool/new_tap.rb deleted file mode 100644 index 1dc7431..0000000 --- a/forester/ruby/evoruby/lib/evo/tool/new_tap.rb +++ /dev/null @@ -1,167 +0,0 @@ -# -# = lib/evo/apps/ - class -# -# Copyright:: Copyright (C) 2009 Christian M. Zmasek -# License:: GNU Lesser General Public License (LGPL) -# -# $Id: new_tap.rb,v 1.4 2010/12/13 19:00:11 cmzmasek Exp $ - - -require 'lib/evo/util/util' -require 'lib/evo/msa/msa_factory' -require 'lib/evo/msa/msa' -require 'lib/evo/io/msa_io' -require 'lib/evo/io/parser/fasta_parser' -require 'lib/evo/io/parser/general_msa_parser' -require 'lib/evo/io/writer/fasta_writer' -require 'lib/evo/io/writer/phylip_sequential_writer' -require 'lib/evo/util/command_line_arguments' - -module Evoruby - - class TaxonomyProcessor - - PRG_NAME = "" - PRG_DATE = "2009.10.09" - PRG_DESC = "replacement of labels in multiple sequence files" - PRG_VERSION = "1.00" - COPYRIGHT = "2009 Christian M Zmasek" - CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" - - REMOVE_REDUNDANT_SEQS_OPTION = "rr" - - def initialize() - @taxonomies = Hash.new() - end - - def run() - - Util.print_program_information( PRG_NAME, - PRG_VERSION, - PRG_DESC, - PRG_DATE, - COPYRIGHT, - CONTACT, - WWW, - STDOUT ) - - if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 ) ) - puts( "Usage: #{PRG_NAME}.rb " ) - puts() - puts( " options: -" + REMOVE_REDUNDANT_SEQS_OPTION + ": to remove redundant sequences" ) - puts() - exit( -1 ) - end - - begin - cla = CommandLineArguments.new( ARGV ) - rescue ArgumentError => e - Util.fatal_error( PRG_NAME, "error: " + e.to_s ) - end - - input = cla.get_file_name( 0 ) - output = cla.get_file_name( 1 ) - map_file = cla.get_file_name( 2 ) - - allowed_opts = Array.new - allowed_opts.push( REMOVE_REDUNDANT_SEQS_OPTION ) - - disallowed = cla.validate_allowed_options_as_str( allowed_opts ) - if ( disallowed.length > 0 ) - Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed ) - end - - - remove_redudant = false - if ( cla.is_option_set?( REMOVE_REDUNDANT_SEQS_OPTION ) ) - remove_redudant = true - end - - if ( File.exists?( output ) ) - Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" ) - end - if ( File.exists?( map_file ) ) - Util.fatal_error( PRG_NAME, "map file [" + map_file + "] already exists" ) - end - if ( !File.exists?( input) ) - Util.fatal_error( PRG_NAME, "infile [" + input + "] does not exist" ) - end - - fasta_like = Util.looks_like_fasta?( input ) - - puts() - puts( "Input alignment : " + input ) - puts( "Output alignment: " + output ) - puts( "Output map : " + map_file ) - if ( fasta_like ) - puts( "Format : Fasta" ) - else - puts( "Format : Phylip like" ) - end - puts() - - species_map = Hash.new - - f = MsaFactory.new() - begin - if ( fasta_like ) - msa = f.create_msa_from_file( input, FastaParser.new() ) - else - msa = f.create_msa_from_file( input, GeneralMsaParser.new() ) - end - rescue Exception => e - Util.fatal_error( PRG_NAME, "failed to read file: " + e.to_s ) - end - - if ( msa == nil || msa.get_number_of_seqs() < 1 ) - Util.fatal_error( PRG_NAME, "failed to read MSA" ) - end - begin - Util.check_file_for_writability( map_file ) - rescue Exception => e - Util.fatal_error( PRG_NAME, "error: " + e.to_, STDOUT ) - end - - if ( remove_redudant ) - removed = msa.remove_redundant_sequences!( true ) - if removed.size > 0 - Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" ) - removed.each { | seq_name | - puts seq_name - } - Util.print_message( PRG_NAME, "will process " + msa.get_number_of_seqs.to_s + " non redundant sequences" ) - end - end - - lf = File.open( map_file, "a" ) - for i in 0 ... msa.get_number_of_seqs - seq = msa.get_sequence( i ) - end - - io = MsaIO.new() - w = nil - if ( fasta_like ) - w = FastaWriter.new() - else - w = PhylipSequentialWriter.new() - end - w.set_max_name_length( 10 ) - w.clean( true ) - begin - io.write_to_file( msa, output, w ) - rescue Exception => e - Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s ) - end - lf.close() - if ( @taxonomies.length > 0 ) - Util.print_message( PRG_NAME, "number of unique taxonomies: " + @taxonomies.length.to_s ) - end - Util.print_message( PRG_NAME, "wrote: " + map_file ) - Util.print_message( PRG_NAME, "wrote: " + output ) - Util.print_message( PRG_NAME, "OK" ) - end - - end # class - -end # module Evoruby \ No newline at end of file