From: cmzmasek Date: Sat, 18 Feb 2017 01:03:02 +0000 (-0800) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2a165043be7f54dc4445bf4332a1af5283711fdf;p=jalview.git in progress... --- diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb index 5186bf5..89e0fe7 100644 --- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb @@ -3,6 +3,8 @@ # # Copyright:: Copyright (C) 2017 Christian M. Zmasek # License:: GNU Lesser General Public License (LGPL) +# +# Last modified: 2017/02/16 require 'lib/evo/util/constants' require 'lib/evo/msa/msa_factory' @@ -75,55 +77,94 @@ module Evoruby ld = Constants::LINE_DELIMITER - domain_pass_counter = 0 - domain_fail_counter = 0 - proteins_with_failing_domains = 0 + domain_pass_counter = 0 + domain_fail_counter = 0 + proteins_with_failing_domains = 0 + domain_not_present_counter = 0 + protein_counter = 1 max_domain_copy_number_per_protein = -1 max_domain_copy_number_sequence = "" + passing_target_length_sum = 0 + overall_target_length_sum = 0 + overall_target_length_min = 10000000 + overall_target_length_max = 0 + passing_target_length_min = 10000000 + passing_target_length_max = 0 hmmscan_datas = [] hmmscan_parser = HmmscanParser.new( hmmscan_output ) results = hmmscan_parser.parse + prev_query = nil + saw_target = false + results.each do | r | + + if ( prev_query != nil ) && ( r.query != prev_query ) + protein_counter += 1 + if !saw_target + log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld + domain_not_present_counter += 1 + end + saw_target = false + end + + prev_query = r.query + if domain_id != r.model next end + saw_target = true + sequence = r.query number = r.number out_of = r.out_of env_from = r.env_from env_to = r.env_to i_e_value = r.i_e_value + prev_query = r.query + + length = env_to - env_from + 1 + + overall_target_length_sum += length + if length > overall_target_length_max + overall_target_length_max = length + end + if length < overall_target_length_min + overall_target_length_min = length + end if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) && - ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) ) + ( ( length_threshold <= 0 ) || ( length >= length_threshold.to_f ) ) ) hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value ) + passing_target_length_sum += length + if length > passing_target_length_max + passing_target_length_max = length + end + if length < passing_target_length_min + passing_target_length_min = length + end if ( number > max_domain_copy_number_per_protein ) max_domain_copy_number_sequence = sequence max_domain_copy_number_per_protein = number end - else # failed - print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" ) - log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" + else # no pass + log << domain_fail_counter.to_s + ": " + sequence.to_s + " fails threshold(s)" if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) ) - print( " iE=" + i_e_value.to_s ) log << " iE=" + i_e_value.to_s end if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f ) le = env_to - env_from + 1 - print( " l=" + le.to_s ) log << " l=" + le.to_s end - print( ld ) log << ld - domain_fail_counter += 1 + domain_fail_counter += 1 end if number > out_of - error_msg = "number > out_of ! (this should not have happened)" + error_msg = "number > out_of (this should not have happened)" raise StandardError, error_msg end @@ -152,7 +193,7 @@ module Evoruby error_msg = "this should not have happened" raise StandardError, error_msg end - else + else # no pass if failed_seqs.find_by_name_start( sequence, true ).length < 1 add_sequence( sequence, in_msa, failed_seqs ) proteins_with_failing_domains += 1 @@ -163,6 +204,12 @@ module Evoruby end hmmscan_datas.clear end + + end # results.each do | r | + + if (prev_query != nil) && (!saw_target) + log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld + domain_not_present_counter += 1 end if domain_pass_counter < 1 @@ -170,14 +217,53 @@ module Evoruby raise IOError, error_msg end + if ( domain_not_present_counter + passed_seqs.get_number_of_seqs + proteins_with_failing_domains ) != protein_counter + error_msg = "not present + passing + not passing != proteins in sequence (fasta) file (this should not have happened)" + raise StandardError, error_msg + end + + puts + log << ld + + log << ld + avg_pass = ( passing_target_length_sum / domain_pass_counter ) + puts( "Passing target domain lengths: average: " + avg_pass.to_s ) + log << "Passing target domain lengths: average: " + avg_pass.to_s + log << ld + puts( "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s) + log << "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + "-" + passing_target_length_max.to_s + log << ld + puts( "Passing target domain lengths: sum: " + domain_pass_counter.to_s ) + log << "Passing target domain lengths: sum: " + domain_pass_counter.to_s + log << ld + log << ld + puts + sum = domain_pass_counter + domain_fail_counter + avg_all = overall_target_length_sum / sum + puts( "All target domain lengths: average: " + avg_all.to_s ) + log << "All target domain lengths: average: " +avg_all.to_s + log << ld + puts( "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s) + log << "All target domain lengths: min-max: " + overall_target_length_min.to_s + "-" + overall_target_length_max.to_s + log << ld + puts( "All target domain lengths: sum: " + sum.to_s ) + log << "All target domain lengths: sum: " + sum.to_s + + puts + puts( "Proteins with passing target domain(s): " + passed_seqs.get_number_of_seqs.to_s ) + puts( "Proteins with no passing target domain: " + proteins_with_failing_domains.to_s ) + puts( "Proteins with no target domain : " + domain_not_present_counter.to_s ) + + log << ld log << ld - puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s ) - log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s + puts + puts( "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s ) + log << "Max target domain copy number per protein (includes non-passing): " + max_domain_copy_number_per_protein.to_s log << ld if ( max_domain_copy_number_per_protein > 1 ) - puts( "First protein with this copy number: " + max_domain_copy_number_sequence ) - log << "First protein with this copy number: " + max_domain_copy_number_sequence + puts( "First target protein with this copy number: " + max_domain_copy_number_sequence ) + log << "First target protein with this copy number: " + max_domain_copy_number_sequence log << ld end @@ -232,22 +318,24 @@ module Evoruby end log << ld - log << "passing domains : " + domain_pass_counter.to_s + ld - log << "failing domains : " + domain_fail_counter.to_s + ld - log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld - log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld - log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld + log << "passing target domains : " + domain_pass_counter.to_s + ld + log << "failing target domains : " + domain_fail_counter.to_s + ld + log << "proteins in sequence (fasta) file : " + in_msa.get_number_of_seqs.to_s + ld + log << "proteins in hmmscan outputfile : " + protein_counter.to_s + ld + log << "proteins with passing target domain(s) : " + passed_seqs.get_number_of_seqs.to_s + ld + log << "proteins with no passing target domain : " + proteins_with_failing_domains.to_s + ld + log << "proteins with no target domain : " + domain_not_present_counter.to_s + ld if min_linker - log << "min linker length : " + min_linker.to_s + ld - log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld - log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld - log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld - log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld - log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld + log << "min linker length : " + min_linker.to_s + ld + log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld + log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld + log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld + log << "proteins with single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld + log << "proteins with close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld end log << ld @@ -473,7 +561,7 @@ module Evoruby error_msg = "sequence \"" + sequence + "\" not unique in sequence file" raise IOError, error_msg end - # hmmsearch is 1 based, wheres sequences are 0 bases in this package. + # hmmscan is 1 based, whereas sequences are 0 bases in this package. seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 ) orig_name = seq.get_name diff --git a/forester/ruby/evoruby/lib/evo/tool/domain_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/domain_sequence_extractor.rb index ac03d43..e7d9865 100644 --- a/forester/ruby/evoruby/lib/evo/tool/domain_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/domain_sequence_extractor.rb @@ -18,6 +18,9 @@ module Evoruby PRG_DATE = "20170214" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" + E_VALUE_THRESHOLD_DEFAULT = 0.1 + LENGTH_THRESHOLD_DEFAULT = 50 + E_VALUE_THRESHOLD_OPTION = 'e' LENGTH_THRESHOLD_OPTION = 'l' ADD_POSITION_OPTION = 'p' @@ -73,7 +76,7 @@ module Evoruby STDOUT ) end - e_value_threshold = 0.1 + e_value_threshold = E_VALUE_THRESHOLD_DEFAULT if ( cla.is_option_set?( E_VALUE_THRESHOLD_OPTION ) ) begin e_value_threshold = cla.get_option_value_as_float( E_VALUE_THRESHOLD_OPTION ) @@ -85,7 +88,7 @@ module Evoruby end end - length_threshold = 50 + length_threshold = LENGTH_THRESHOLD_DEFAULT if ( cla.is_option_set?( LENGTH_THRESHOLD_OPTION ) ) begin length_threshold = cla.get_option_value_as_int( LENGTH_THRESHOLD_OPTION ) @@ -164,41 +167,40 @@ module Evoruby ld = Constants::LINE_DELIMITER puts() - puts( "Domain : " + domain_id ) - log << "Domain : " + domain_id + ld - puts( "Hmmscan outputfile : " + hmmscan_output ) - log << "Hmmscan outputfile : " + hmmscan_output + ld - puts( "Fasta sequencefile (complete sequences): " + fasta_sequence_file ) - log << "Fasta sequencefile (complete sequences): " + fasta_sequence_file + ld - puts( "Outputfile : " + outfile + ".fasta" ) - log << "Outputfile : " + outfile + ld - puts( "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX ) - log << "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX + ld - puts( "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX ) - log << "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX + ld - puts( "Logfile : " + outfile + LOG_FILE_SUFFIX ) - log << "Logfile : " + outfile + LOG_FILE_SUFFIX + ld + puts( "Domain : " + domain_id ) + log << "Domain : " + domain_id + ld + puts( "Hmmscan outputfile : " + hmmscan_output ) + log << "Hmmscan outputfile : " + hmmscan_output + ld + puts( "Fasta sequencefile (complete sequences) : " + fasta_sequence_file ) + log << "Fasta sequencefile (complete sequences) : " + fasta_sequence_file + ld + puts( "Outputfile : " + outfile + ".fasta" ) + log << "Outputfile : " + outfile + ld + puts( "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX ) + log << "Passed sequences outfile (fasta) : " + outfile + PASSED_SEQS_SUFFIX + ld + puts( "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX ) + log << "Failed sequences outfile (fasta) : " + outfile + FAILED_SEQS_SUFFIX + ld + puts( "Logfile : " + outfile + LOG_FILE_SUFFIX ) + log << "Logfile : " + outfile + LOG_FILE_SUFFIX + ld if ( e_value_threshold >= 0.0 ) - puts( "E-value threshold : " + e_value_threshold.to_s ) - log << "E-value threshold : " + e_value_threshold.to_s + ld + puts( "iE-value threshold : " + e_value_threshold.to_s ) + log << "iE-value threshold : " + e_value_threshold.to_s + ld else - puts( "E-value threshold : no threshold" ) - log << "E-value threshold : no threshold" + ld + puts( "iE-value threshold : no threshold" ) + log << "iE-value threshold : no threshold" + ld end if ( length_threshold > 0 ) - puts( "Length threshold : " + length_threshold.to_s ) - log << "Length threshold : " + length_threshold.to_s + ld + puts( "Length threshold (env) : " + length_threshold.to_s ) + log << "Length threshold (env) : " + length_threshold.to_s + ld else - puts( "Length threshold : no threshold" ) - log << "Length threshold : no threshold" + ld + puts( "Length threshold (env) : no threshold" ) + log << "Length threshold (env) : no threshold" + ld end - if ( add_position ) - puts( "Add positions (rel to complete seq) to extracted domains: true" ) - log << "Add positions (rel to complete seq) to extracted domains: true" + ld + puts( "Add positions (rel to complete seq) to extracted domains : true" ) + log << "Add positions (rel to complete seq) to extracted domains : true" + ld else - puts( "Add positions (rel to complete seq) to extracted domains: false" ) - log << "Add positions (rel to complete seq) to extracted domains: false" + ld + puts( "Add positions (rel to complete seq) to extracted domains : false" ) + log << "Add positions (rel to complete seq) to extracted domains : false" + ld end if ( add_domain_number ) @@ -210,6 +212,7 @@ module Evoruby end puts + log << ld domain_count = 0 begin @@ -238,10 +241,10 @@ module Evoruby puts Util.print_message( PRG_NAME, "extracted a total of " + domain_count.to_s + " domains" ) - Util.print_message( PRG_NAME, "wrote; " + outfile + ".fasta") - Util.print_message( PRG_NAME, "wrote: " + outfile + LOG_FILE_SUFFIX ) - Util.print_message( PRG_NAME, "wrote: " + outfile + PASSED_SEQS_SUFFIX ) - Util.print_message( PRG_NAME, "wrote: " + outfile + FAILED_SEQS_SUFFIX ) + Util.print_message( PRG_NAME, "wrote: " + outfile + ".fasta") + Util.print_message( PRG_NAME, "wrote: " + outfile + LOG_FILE_SUFFIX ) + Util.print_message( PRG_NAME, "wrote: " + outfile + PASSED_SEQS_SUFFIX ) + Util.print_message( PRG_NAME, "wrote: " + outfile + FAILED_SEQS_SUFFIX ) begin f = File.open( outfile + LOG_FILE_SUFFIX, 'a' ) @@ -261,10 +264,10 @@ module Evoruby puts() puts( "Usage:" ) puts() - puts( " " + PRG_NAME + ".rb [options] [file containing complete sequences in fasta format] [outputfile]" ) + puts( " " + PRG_NAME + ".rb [options] [file containing complete sequences in fasta format] [outputfile]" ) puts() - puts( " options: -" + E_VALUE_THRESHOLD_OPTION + "= : iE-value threshold, default is 0.1" ) - puts( " -" + LENGTH_THRESHOLD_OPTION + "= : length threshold, default is 50" ) + puts( " options: -" + E_VALUE_THRESHOLD_OPTION + "= : iE-value threshold for target domain, default is " + E_VALUE_THRESHOLD_DEFAULT.to_s ) + puts( " -" + LENGTH_THRESHOLD_OPTION + "= : length threshold target domain (env), default is " + LENGTH_THRESHOLD_DEFAULT.to_s ) puts( " -" + ADD_DOMAIN_NUMBER_OPTION + " : to add numbers to extracted domains (in case of more than one domain per complete seq) (example \"domain~2-3\")" ) puts( " -" + ADD_POSITION_OPTION + " : to add positions (rel to complete seq) to extracted domains" ) puts( " -" + ADD_SPECIES + " : to add species [in brackets]" ) diff --git a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb index d952277..57b5336 100644 --- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb @@ -9,7 +9,6 @@ require 'date' require 'set' - require 'lib/evo/util/constants' require 'lib/evo/util/util' require 'lib/evo/util/command_line_arguments' @@ -23,17 +22,13 @@ require 'lib/evo/io/parser/general_msa_parser' require 'lib/evo/io/writer/msa_writer' module Evoruby - class MsaProcessor PRG_NAME = "msa_pro" - PRG_DATE = "131112" + PRG_DATE = "170215" PRG_DESC = "processing of multiple sequence alignments" PRG_VERSION = "1.08" - COPYRIGHT = "2008-2010 Christian M Zmasek" - CONTACT = "phylosoft@gmail.com" - WWW = "www.phylosoft.org" - + WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" NAME_LENGTH_DEFAULT = 10 WIDTH_DEFAULT_FASTA = 60 @@ -61,8 +56,6 @@ module Evoruby LOG_SUFFIX = "_msa_pro.log" HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" - - def initialize() @input_format_set = false @output_format_set = false @@ -95,17 +88,14 @@ module Evoruby @last = -1 end - def run() Util.print_program_information( PRG_NAME, - PRG_VERSION, - PRG_DESC, - PRG_DATE, - COPYRIGHT, - CONTACT, - WWW, - STDOUT ) + PRG_VERSION, + PRG_DESC, + PRG_DATE, + WWW, + STDOUT ) if ( ARGV == nil || ARGV.length < 1 ) Util.print_message( PRG_NAME, "Illegal number of arguments" ) @@ -120,7 +110,7 @@ module Evoruby end if ( cla.is_option_set?( HELP_OPTION_1 ) || - cla.is_option_set?( HELP_OPTION_2 ) ) + cla.is_option_set?( HELP_OPTION_2 ) ) print_help exit( 0 ) end @@ -155,7 +145,7 @@ module Evoruby disallowed = cla.validate_allowed_options_as_str( allowed_opts ) if ( disallowed.length > 0 ) Util.fatal_error( PRG_NAME, - "unknown option(s): " + disallowed ) + "unknown option(s): " + disallowed ) end input = cla.get_file_name( 0 ) @@ -430,8 +420,6 @@ module Evoruby msa = sort( msa ) end - - if ( @split > 0 ) begin msas = msa.split( @split, true ) @@ -518,8 +506,8 @@ module Evoruby if removed.size > 0 identicals = msa.get_identical_seqs_detected log << "the following " + identicals.size.to_s + " sequences are identical:" + ld - identicals.each { | s | - log << s + ld + identicals.each { | identical | + log << identical + ld } log << "ignoring the following " + removed.size.to_s + " redundant sequences:" + ld removed.each { | seq_name | @@ -576,13 +564,11 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end - end Util.print_message( PRG_NAME, "OK" ) puts end - private def sort( msa ) @@ -604,77 +590,94 @@ module Evoruby @fasta_input = fi @input_format_set = true end + def set_phylip_input( pi = true ) @phylip_input = pi @input_format_set = true end + def set_name_length( i ) @name_length = i @name_length_set = true end + def set_width( i ) @width = i end + def set_fasta_output( fo = true ) @fasta_output = fo @output_format_set = true end + def set_pi_output( pso = true ) @pi_output = pso @output_format_set = true end + def set_nexus_output( nexus = true ) @nexus_output = nexus @output_format_set = true end + def set_clean( c = true ) @clean = c end + def set_remove_gap_columns( rgc = true ) @rgc = rgc end + def set_remove_gap_only_columns( rgoc = true ) @rgoc = rgoc end + def set_remove_gaps( rg = true ) @rg = rg end + def set_remove_gap_ratio( rgr ) @rgr = rgr end + def set_remove_seqs_gap_ratio( rsgr ) @rsgr = rsgr end + def set_remove_seqs_min_non_gap_length( rsl ) @rsl = rsl end + def set_remove_seqs( file ) @seqs_name_file = file @remove_seqs = true @keep_seqs = false end + def set_keep_seqs( file ) @seqs_name_file = file @keep_seqs = true @remove_seqs = false end + def set_trim( first, last ) @trim = true @first = first @last = last end + def set_remove_matching( remove ) @remove_matching = remove end + def set_keep_matching( keep ) @keep_matching = keep end + def set_rem_red( rr ) @rem_red = rr end - - def set_split( s ) if ( s > 0 ) @split = s @@ -843,7 +846,6 @@ module Evoruby @die_if_name_too_long = true end - end def print_help() @@ -875,11 +877,6 @@ module Evoruby puts() end - - - - end # class MsaProcessor - end # module Evoruby diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index cbbff63..06c103e 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -32,7 +32,7 @@ module Evoruby DOMAINS_MAPFILE_SUFFIX = '_hmmscan_10.dff' SLEEP_TIME = 0.05 REMOVE_NI = true - IDS_ONLY = true #TODO this should be a command line option + IDS_ONLY = false #TODO this should be a command line option FIXED_NIM_FILE = 'all.nim' #TODO this should be a command line option TMP_FILE_1 = '___PD1___' TMP_FILE_2 = '___PD2___' @@ -44,8 +44,6 @@ module Evoruby PRG_DATE = "170209" PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures" PRG_VERSION = "1.02" - COPYRIGHT = "2017 Christian M Zmasek" - CONTACT = "phyloxml at gmail dot com" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" HELP_OPTION_1 = "help" @@ -58,8 +56,6 @@ module Evoruby PRG_VERSION, PRG_DESC, PRG_DATE, - COPYRIGHT, - CONTACT, WWW, STDOUT ) @@ -122,10 +118,10 @@ module Evoruby log << 'input suffix : ' + in_suffix + NL log << 'output suffix : ' + out_suffix + NL - if ( File.exists?( TMP_FILE_1 ) ) + if ( File.exist?( TMP_FILE_1 ) ) File.delete( TMP_FILE_1 ) end - if ( File.exists?( TMP_FILE_2 ) ) + if ( File.exist?( TMP_FILE_2 ) ) File.delete( TMP_FILE_2 ) end