From: cmzmasek Date: Wed, 29 Mar 2017 04:08:07 +0000 (-0700) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=834185a6ee91c58ea3263043a61c9444fb2d6463;p=jalview.git in progress --- diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 5bc5bac..a7867f6 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -32,7 +32,6 @@ module Evoruby DOMAINS_MAPFILE_SUFFIX = '.dff' SLEEP_TIME = 0.05 REMOVE_NI = true - IDS_ONLY = false #TODO this should be a command line option FIXED_NIM_FILE = nil #'all.nim' #TODO this should be a command line option TMP_FILE_1 = '___PD1___' TMP_FILE_2 = '___PD2___' @@ -48,6 +47,7 @@ module Evoruby HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" + NO_DOMAINS_OPTION = 'nd' NL = Constants::LINE_DELIMITER def run @@ -59,7 +59,7 @@ module Evoruby WWW, STDOUT ) - if ( ARGV == nil || ARGV.length > 3 || ARGV.length < 2 ) + if ( ARGV == nil || ARGV.length < 2 ) print_help exit( -1 ) end @@ -92,6 +92,26 @@ module Evoruby exit( 0 ) end + if ( cla.get_number_of_files != 2 ) + print_help + exit( -1 ) + end + + allowed_opts = Array.new + allowed_opts.push(NO_DOMAINS_OPTION) + + disallowed = cla.validate_allowed_options_as_str( allowed_opts ) + if ( disallowed.length > 0 ) + Util.fatal_error( PRG_NAME, + "unknown option(s): " + disallowed, + STDOUT ) + end + + no_domains = false + if cla.is_option_set?(NO_DOMAINS_OPTION) + no_domains = true + end + if File.exist?( LOG_FILE ) Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' ) end @@ -178,48 +198,45 @@ module Evoruby ids_mapfile_name = FIXED_NIM_FILE end + begin + Util.check_file_for_readability( ids_mapfile_name ) + rescue IOError + Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! ) + end Util.print_message( PRG_NAME, "Ids mapfile: " + ids_mapfile_name ) log << "Ids mapfile: " + ids_mapfile_name + NL - unless IDS_ONLY - domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX ) - seqs_file_name = get_seq_file( files, phylogeny_id ) - Util.print_message( PRG_NAME, "Domains file: " + domains_mapfile_name ) - log << "Domains file: " + domains_mapfile_name + NL - Util.print_message( PRG_NAME, "Seq file: " + seqs_file_name ) - log << "Seq file: " + seqs_file_name + NL + seqs_file_name = get_seq_file( files, phylogeny_id ) + begin + Util.check_file_for_readability( seqs_file_name ) + rescue IOError + Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! ) end + Util.print_message( PRG_NAME, "Seq file: " + seqs_file_name ) + log << "Seq file: " + seqs_file_name + NL - unless IDS_ONLY + unless no_domains + domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX ) begin Util.check_file_for_readability( domains_mapfile_name ) rescue IOError Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! ) end - begin - Util.check_file_for_readability( seqs_file_name ) - rescue IOError - Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! ) - end + Util.print_message( PRG_NAME, "Domains file: " + domains_mapfile_name ) + log << "Domains file: " + domains_mapfile_name + NL end + cmd = decorator + + ' -t -p -f=m ' + phylogeny_file + ' ' + + seqs_file_name + ' ' + TMP_FILE_1 + puts cmd begin - Util.check_file_for_readability( ids_mapfile_name ) - rescue IOError - Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! ) + execute_cmd( cmd, log ) + rescue Error + Util.fatal_error( PRG_NAME, 'error: ' + $! ) end - unless IDS_ONLY - cmd = decorator + - ' -t -p -f=m ' + phylogeny_file + ' ' + - seqs_file_name + ' ' + TMP_FILE_1 - puts cmd - begin - execute_cmd( cmd, log ) - rescue Error - Util.fatal_error( PRG_NAME, 'error: ' + $! ) - end - + unless no_domains cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + '-f=d ' + TMP_FILE_1 + ' ' + domains_mapfile_name + ' ' + TMP_FILE_2 @@ -231,9 +248,9 @@ module Evoruby end end - if IDS_ONLY + if no_domains cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + - '-f=n ' + phylogeny_file + ' ' + + '-f=n ' + TMP_FILE_1 + ' ' + ids_mapfile_name + ' ' + outfile puts cmd begin @@ -241,6 +258,7 @@ module Evoruby rescue Error Util.fatal_error( PRG_NAME, 'error: ' + $! ) end + File.delete( TMP_FILE_1 ) else cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + '-f=n ' + TMP_FILE_2 + ' ' + @@ -274,7 +292,9 @@ module Evoruby end def get_id( phylogeny_file_name ) - if phylogeny_file_name =~ /^(.+?)_/ + if phylogeny_file_name =~ /^(.+?_DA)_/ + return $1 + elsif phylogeny_file_name =~ /^(.+?)_/ return $1 end nil @@ -318,11 +338,18 @@ module Evoruby end def print_help() - puts( "Usage:" ) - puts() - puts( " " + PRG_NAME + ".rb " ) - puts() - puts() + puts 'Usage:' + puts + puts " " + PRG_NAME + ".rb " + puts + puts " required files (in this dir): " + "name mappings : .nim" + puts " " + "sequences : _ni.fasta" + puts " " + "domain architectures: .dff" + puts + puts " options: -" + NO_DOMAINS_OPTION + ": to not add domain architecture information (.dff file)" + puts + puts "Example: " + PRG_NAME + ".rb .xml _d.xml" + puts end end # class PhylogenyiesDecorator