From: cmzmasek@gmail.com Date: Fri, 15 Nov 2013 23:58:42 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b2da9d4556ac5b90e50d1460040f7387140dd49b;p=jalview.git inprogress --- diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 6006729..953f924 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -24,7 +24,7 @@ module Evoruby #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn' #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn' - DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc -mp -or' + DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -tc -mp -or' # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA" #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1' #DECORATOR_OPTIONS_DOMAINS = '-r=1' @@ -33,7 +33,8 @@ module Evoruby DOMAINS_MAPFILE_SUFFIX = '.dff' SLEEP_TIME = 0.1 REMOVE_NI = true - TMP_FILE = '___PD___' + TMP_FILE_1 = '___PD1___' + TMP_FILE_2 = '___PD2___' LOG_FILE = '00_phylogenies_decorator.log' FORESTER_HOME = ENV[Constants::FORESTER_HOME_ENV_VARIABLE] JAVA_HOME = ENV[Constants::JAVA_HOME_ENV_VARIABLE] @@ -46,8 +47,7 @@ module Evoruby CONTACT = "phylosoft@gmail.com" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" - IDS_ONLY_OPTION = "n" - DOMAINS_ONLY_OPTION = "d" + HELP_OPTION_1 = "help" HELP_OPTION_2 = "h" @@ -146,8 +146,11 @@ module Evoruby log << 'input suffix : ' + in_suffix + NL log << 'output suffix : ' + out_suffix + NL - if ( File.exists?( TMP_FILE ) ) - File.delete( TMP_FILE ) + if ( File.exists?( TMP_FILE_1 ) ) + File.delete( TMP_FILE_1 ) + end + if ( File.exists?( TMP_FILE_2 ) ) + File.delete( TMP_FILE_2 ) end files = Dir.entries( "." ) @@ -189,61 +192,52 @@ module Evoruby ids_mapfile_name = nil domains_mapfile_name = nil + seqs_file_name = nil - if ids_only - ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX ) - elsif domains_only - domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX ) - else - ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX ) - domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX ) - end + ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX ) + domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX ) + seqs_file_name = get_seq_file( files, phylogeny_id ) - if domains_mapfile_name != nil - begin - Util.check_file_for_readability( domains_mapfile_name ) - rescue ArgumentError - Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! ) - end - end - if ids_mapfile_name != nil - begin - Util.check_file_for_readability( ids_mapfile_name ) - rescue ArgumentError - Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! ) - end + begin + Util.check_file_for_readability( domains_mapfile_name ) + rescue ArgumentError + Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! ) end - if domains_mapfile_name != nil - if ids_mapfile_name != nil - my_outfile = TMP_FILE - else - my_outfile = outfile - end - cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + - '-f=d ' + phylogeny_file + ' ' + - domains_mapfile_name + ' ' + my_outfile - puts cmd - execute_cmd( cmd, log ) + begin + Util.check_file_for_readability( ids_mapfile_name ) + rescue ArgumentError + Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! ) end - if ids_mapfile_name != nil - if domains_mapfile_name != nil - my_infile = TMP_FILE - else - my_infile = phylogeny_file - end - cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + - '-f=n ' + my_infile + ' ' + - ids_mapfile_name + ' ' + outfile - puts cmd - execute_cmd( cmd, log ) + begin + Util.check_file_for_readability( seqs_file_name ) + rescue ArgumentError + Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! ) end - if ( File.exists?( TMP_FILE ) ) - File.delete( TMP_FILE ) - end + cmd = decorator + + ' -p -f=m ' + phylogeny_file + ' ' + + seqs_file_name + ' ' + TMP_FILE_1 + puts cmd + execute_cmd( cmd, log ) + + cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + + '-f=d ' + TMP_FILE_1 + ' ' + + domains_mapfile_name + ' ' +TMP_FILE_2 + puts cmd + execute_cmd( cmd, log ) + + cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + + '-f=n ' + TMP_FILE_2 + ' ' + + ids_mapfile_name + ' ' + outfile + puts cmd + execute_cmd( cmd, log ) + + File.delete( TMP_FILE_1 ) + File.delete( TMP_FILE_2 ) + end } open( LOG_FILE, 'w' ) do | f | @@ -302,13 +296,35 @@ module Evoruby matching_files[ 0 ] end + def get_seq_file( files_in_dir, phylogeny_id ) + matching_files = Array.new + + files_in_dir.each { | file | + + if ( !File.directory?( file ) && + file !~ /^\./ && + file !~ /^00/ && + file =~ /^#{phylogeny_id}.+\d$/ ) + matching_files << file + end + + } + + if matching_files.length < 1 + Util.fatal_error( PRG_NAME, 'no seq file matching [' + phylogeny_id + '] present in current directory' ) + end + if matching_files.length > 1 + Util.fatal_error( PRG_NAME, 'more than one seq file matching [' + phylogeny_id + '] present in current directory' ) + end + matching_files[ 0 ] + end + + def print_help() puts( "Usage:" ) puts() - puts( " " + PRG_NAME + ".rb [options] " ) + puts( " " + PRG_NAME + ".rb " ) puts() - puts( " options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" ) - puts( " -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures only" ) puts() end end # class PhylogenyiesDecorator