# $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
#
# Environment variable FORESTER_HOME needs to point to the appropriate
-# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/)
+# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/)
require 'lib/evo/util/constants'
require 'lib/evo/util/util'
module Evoruby
- class PhylogeniesDecorator
-
- DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
- # -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'
- IDS_MAPFILE_SUFFIX = '.nim'
- DOMAINS_MAPFILE_SUFFIX = '.dff'
- SLEEP_TIME = 0.1
- REMOVE_NI = true
- TMP_FILE = '___PD___'
- 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 = "2008.09.02"
- PRG_DESC = "decoration of phylogenies with sequence/species names and domain architectures"
- PRG_VERSION = "1.0.1"
- COPYRIGHT = "2008-2009 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
-
- IDS_ONLY_OPTION = "n"
- DOMAINS_ONLY_OPTION = "d"
- HELP_OPTION_1 = "help"
- HELP_OPTION_2 = "h"
-
- NL = Constants::LINE_DELIMITER
-
- 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 < 2 )
- print_help
- exit( -1 )
- end
-
- if FORESTER_HOME == nil || FORESTER_HOME.length < 1
- Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::FORESTER_HOME_ENV_VARIABLE} has not been set" )
- end
- if JAVA_HOME == nil || JAVA_HOME.length < 1
- Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::JAVA_HOME_ENV_VARIABLE} has not been set" )
- end
-
- if !File.exist?( FORESTER_HOME )
- Util.fatal_error( PRG_NAME, '[' + FORESTER_HOME + '] does not exist' )
- end
- if !File.exist?( JAVA_HOME )
- Util.fatal_error( PRG_NAME, '[' + JAVA_HOME + '] does not exist' )
- end
-
- decorator = JAVA_HOME + '/bin/java -cp ' + FORESTER_HOME + '/java/forester.jar org.forester.application.decorator'
-
- begin
- cla = CommandLineArguments.new( ARGV )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
- end
-
- if ( cla.is_option_set?( HELP_OPTION_1 ) ||
- cla.is_option_set?( HELP_OPTION_2 ) )
- print_help
- exit( 0 )
- end
-
- if File.exist?( LOG_FILE )
- 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
- log << "Program : " + PRG_NAME + NL
- log << "Version : " + PRG_VERSION + NL
- log << "Program date : " + PRG_DATE + NL
- log << "Options for seq names: " + DECORATOR_OPTIONS_SEQ_NAMES + NL
- log << "Options for domains : " + DECORATOR_OPTIONS_DOMAINS + NL
- log << "FORESTER_HOME : " + FORESTER_HOME + NL
- log << "JAVA_HOME : " + JAVA_HOME + NL + NL
- log << "Date/time: " + now.to_s + NL
- log << "Directory: " + Dir.getwd + NL + NL
-
- Util.print_message( PRG_NAME, 'input suffix : ' + in_suffix )
- Util.print_message( PRG_NAME, 'output suffix : ' + out_suffix )
-
- log << 'input suffix : ' + in_suffix + NL
- log << 'output suffix : ' + out_suffix + NL
-
- if ( File.exists?( TMP_FILE ) )
- File.delete( TMP_FILE )
- end
-
- files = Dir.entries( "." )
-
- counter = 0
-
- files.each { | phylogeny_file |
- if ( !File.directory?( phylogeny_file ) &&
- phylogeny_file !~ /^\./ &&
- phylogeny_file !~ /^00/ &&
- phylogeny_file !~ /#{out_suffix}$/ &&
- phylogeny_file =~ /#{in_suffix}$/ )
- begin
- Util.check_file_for_readability( phylogeny_file )
- rescue ArgumentError
- Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
- end
-
- counter += 1
-
- outfile = phylogeny_file.sub( /#{in_suffix}$/, out_suffix )
-
- if REMOVE_NI
- outfile = outfile.sub( /_ni_/, '_' )
- end
-
- if File.exists?( outfile )
- msg = counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile +
- ' : already exists, skipping'
- Util.print_message( PRG_NAME, msg )
- log << msg + NL
- next
- end
-
- Util.print_message( PRG_NAME, counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile )
- log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
-
- phylogeny_id = get_id( phylogeny_file )
-
- ids_mapfile_name = nil
- domains_mapfile_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
-
- 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
- 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
- execute_cmd( cmd, log )
- 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=s ' + my_infile + ' ' +
- ids_mapfile_name + ' ' + outfile
- execute_cmd( cmd, log )
- end
-
- if ( File.exists?( TMP_FILE ) )
- File.delete( TMP_FILE )
- end
- end
- }
- open( LOG_FILE, 'w' ) do | f |
- f.write( log )
- end
- puts
- Util.print_message( PRG_NAME, 'OK' )
- puts
- end # def run
-
- def execute_cmd( cmd, log )
- log << 'excuting ' + cmd + NL
- IO.popen( cmd , 'r+' ) do | pipe |
- pipe.close_write
- log << pipe.read + NL + NL
- end
- sleep( SLEEP_TIME )
- end
-
+ class PhylogeniesDecorator
+
+ #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
+ #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+ 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 = '_hmmscan_10.dff'
+ SLEEP_TIME = 0.1
+ REMOVE_NI = true
+ 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_DESC = "decoration of phylogenies with sequence/species names and domain architectures"
+ PRG_VERSION = "1.02"
+ COPYRIGHT = "2012 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
+
+
+ HELP_OPTION_1 = "help"
+ HELP_OPTION_2 = "h"
+
+ NL = Constants::LINE_DELIMITER
+
+ 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 < 2 )
+ print_help
+ exit( -1 )
+ end
+
+ if FORESTER_HOME == nil || FORESTER_HOME.length < 1
+ Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::FORESTER_HOME_ENV_VARIABLE} has not been set" )
+ end
+ if JAVA_HOME == nil || JAVA_HOME.length < 1
+ Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::JAVA_HOME_ENV_VARIABLE} has not been set" )
+ end
+
+ if !File.exist?( FORESTER_HOME )
+ Util.fatal_error( PRG_NAME, '[' + FORESTER_HOME + '] does not exist' )
+ end
+ if !File.exist?( JAVA_HOME )
+ Util.fatal_error( PRG_NAME, '[' + JAVA_HOME + '] does not exist' )
+ end
+
+ decorator = JAVA_HOME + '/bin/java -cp ' + FORESTER_HOME + '/java/forester.jar org.forester.application.decorator'
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+ cla.is_option_set?( HELP_OPTION_2 ) )
+ print_help
+ exit( 0 )
+ end
+
+ if File.exist?( LOG_FILE )
+ Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
+ end
+
+ in_suffix = cla.get_file_name( 0 )
+ out_suffix = cla.get_file_name( 1 )
+
+ log = String.new
+
+ now = DateTime.now
+ log << "Program : " + PRG_NAME + NL
+ log << "Version : " + PRG_VERSION + NL
+ log << "Program date : " + PRG_DATE + NL
+ log << "Options for seq names: " + DECORATOR_OPTIONS_SEQ_NAMES + NL
+ log << "Options for domains : " + DECORATOR_OPTIONS_DOMAINS + NL
+ log << "FORESTER_HOME : " + FORESTER_HOME + NL
+ log << "JAVA_HOME : " + JAVA_HOME + NL + NL
+ log << "Date/time: " + now.to_s + NL
+ log << "Directory: " + Dir.getwd + NL + NL
+
+ Util.print_message( PRG_NAME, 'input suffix : ' + in_suffix )
+ Util.print_message( PRG_NAME, 'output suffix : ' + out_suffix )
+
+ log << 'input suffix : ' + in_suffix + NL
+ log << 'output suffix : ' + out_suffix + NL
+
+ 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( "." )
+
+ counter = 0
+
+ files.each { | phylogeny_file |
+ if ( !File.directory?( phylogeny_file ) &&
+ phylogeny_file !~ /^\./ &&
+ phylogeny_file !~ /^00/ &&
+ phylogeny_file !~ /#{out_suffix}$/ &&
+ phylogeny_file =~ /#{in_suffix}$/ )
+ begin
+ Util.check_file_for_readability( phylogeny_file )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
+ end
+
+ counter += 1
+
+ outfile = phylogeny_file.sub( /#{in_suffix}$/, out_suffix )
+
+ if REMOVE_NI
+ outfile = outfile.sub( /_ni_/, '_' )
+ end
+
+ if File.exists?( outfile )
+ msg = counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile +
+ ' : already exists, skipping'
+ Util.print_message( PRG_NAME, msg )
+ log << msg + NL
+ next
+ end
+
+ Util.print_message( PRG_NAME, counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile )
+ log << counter.to_s + ': ' + phylogeny_file + ' -> ' + outfile + NL
+
+ phylogeny_id = get_id( phylogeny_file )
+ puts "id:" + phylogeny_id
+
+ ids_mapfile_name = nil
+ domains_mapfile_name = nil
+ seqs_file_name = nil
+
+ 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 )
+
+
+ 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( ids_mapfile_name )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
+ end
+
+ begin
+ Util.check_file_for_readability( seqs_file_name )
+ rescue ArgumentError
+ Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
+ 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 )
- def get_id( phylogeny_file_name )
- phylogeny_file_name =~ /^([^_]+)/
- $1
end
-
- def get_file( files_in_dir, phylogeny_id, suffix_pattern )
- matching_files = Array.new
- files_in_dir.each { | file |
-
- if ( !File.directory?( file ) &&
- file !~ /^\./ &&
- file !~ /^00/ &&
- file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
- 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
- Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
- '_] [' + suffix_pattern + '] present in current directory' )
- end
- matching_files[ 0 ]
+ }
+ open( LOG_FILE, 'w' ) do | f |
+ f.write( log )
+ end
+ puts
+ Util.print_message( PRG_NAME, 'OK' )
+ puts
+ end # def run
+
+ def execute_cmd( cmd, log )
+ log << 'excuting ' + cmd + NL
+ IO.popen( cmd , 'r+' ) do | pipe |
+ pipe.close_write
+ log << pipe.read + NL + NL
+ end
+ sleep( SLEEP_TIME )
+ end
+
+
+ def get_id( phylogeny_file_name )
+ phylogeny_file_name =~ /^(.+?)__/
+ $1
+ end
+
+ def get_file( files_in_dir, phylogeny_id, suffix_pattern )
+ matching_files = Array.new
+
+ files_in_dir.each { | file |
+
+ if ( !File.directory?( file ) &&
+ file !~ /^\./ &&
+ file !~ /^00/ &&
+ file =~ /^#{phylogeny_id}#{suffix_pattern}$/ )
+ matching_files << file
end
-
- def print_help()
- puts( "Usage:" )
- puts()
- puts( " " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
- puts()
- puts( " options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
- puts( " -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures" )
- puts()
+ }
+ if matching_files.length < 1
+ Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
+ + 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' )
+ 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$/ )
+ matching_files << file
end
- end # class PhylogenyiesDecorator
+ }
+
+ 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 <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
+ puts()
+ puts()
+ end
+ end # class PhylogenyiesDecorator
end # module Evoruby
git://source.jalview.org / jalview.git / blobdiff