X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogenies_decorator.rb;h=6668877e7ecccede4398580798717ce3fdea6c36;hb=36ea5e3d816a5afe5042c28ff0c07394575521f5;hp=4e26acb2f5065ca90931008588acc12972b4fdcf;hpb=fd508ee418219eda297f3a4da5f4d3be7f8a6db8;p=jalview.git diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 4e26acb..6668877 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -24,30 +24,30 @@ module Evoruby #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn' #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn' - DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc' + 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' DECORATOR_OPTIONS_DOMAINS = '-p -t' IDS_MAPFILE_SUFFIX = '.nim' - DOMAINS_MAPFILE_SUFFIX = '.dff' - SLEEP_TIME = 0.1 + DOMAINS_MAPFILE_SUFFIX = '_hmmscan_10.dff' + SLEEP_TIME = 0.05 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] PRG_NAME = "phylogenies_decorator" - PRG_DATE = "2012.10.11" + PRG_DATE = "2013.11.15" PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures" PRG_VERSION = "1.02" - COPYRIGHT = "2012 Christian M Zmasek" + COPYRIGHT = "2013 Christian M Zmasek" 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" @@ -101,32 +101,9 @@ module Evoruby Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' ) end - allowed_opts = Array.new - allowed_opts.push( IDS_ONLY_OPTION ) - allowed_opts.push( DOMAINS_ONLY_OPTION ) - - disallowed = cla.validate_allowed_options_as_str( allowed_opts ) - if ( disallowed.length > 0 ) - Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed ) - end - - ids_only = false - domains_only = false - in_suffix = cla.get_file_name( 0 ) out_suffix = cla.get_file_name( 1 ) - if cla.is_option_set?( IDS_ONLY_OPTION ) - ids_only = true - end - if cla.is_option_set?( DOMAINS_ONLY_OPTION ) - domains_only = true - end - - if ( ids_only && domains_only ) - Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' ) - end - log = String.new now = DateTime.now @@ -146,8 +123,11 @@ 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( "." ) @@ -186,64 +166,58 @@ module Evoruby log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL phylogeny_id = get_id( phylogeny_file ) + puts + + Util.print_message( PRG_NAME, "id: " + phylogeny_id ) + log << "id: " + phylogeny_id + NL 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 + 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 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( ids_mapfile_name ) + rescue ArgumentError + Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_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( seqs_file_name ) + rescue ArgumentError + Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_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 ) - 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 ) - if ( File.exists?( TMP_FILE ) ) - File.delete( TMP_FILE ) - end end } open( LOG_FILE, 'w' ) do | f | @@ -265,38 +239,61 @@ module Evoruby def get_id( phylogeny_file_name ) - phylogeny_file_name =~ /^([^_]+)/ + phylogeny_file_name =~ /^(.+?)__/ $1 end def get_file( files_in_dir, phylogeny_id, suffix_pattern ) matching_files = Array.new + files_in_dir.each { | file | if ( !File.directory?( file ) && file !~ /^\./ && file !~ /^00/ && - file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ ) + file =~ /^#{phylogeny_id}#{suffix_pattern}$/ ) matching_files << file end } if matching_files.length < 1 Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id + - '_] [' + suffix_pattern + '] present in current directory' ) - elsif matching_files.length > 1 + + suffix_pattern + '] present in current directory' ) + end + if matching_files.length > 1 Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id + - '_] [' + suffix_pattern + '] present in current directory' ) + + suffix_pattern + '] present in current directory' ) + end + matching_files[ 0 ] + end + + def get_seq_file( files_in_dir, phylogeny_id ) + matching_files = Array.new + + files_in_dir.each { | file | + + if ( !File.directory?( file ) && + file !~ /^\./ && + file !~ /^00/ && + ( file =~ /^#{phylogeny_id}__.+\d$/ || file =~ /^#{phylogeny_id}__.*\.fasta$/ ) ) + 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" ) puts() end end # class PhylogenyiesDecorator