module Evoruby
- class PhylogenyFactory
-
- PRG_NAME = "phylogeny_factory"
- PRG_DATE = "2010.05.26"
- PRG_DESC = "automated phylogeny reconstruction using queing system"
- PRG_VERSION = "1.1"
- COPYRIGHT = "2010 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
-
- USE_JOB_SUBMISSION_SYSTEM_OPTION = 's'
- LOG_FILE = '00_phylogeny_factory.log'
- TEMPLATE_FILE = '00_phylogeny_factory.template'
- PBS_O_WORKDIR = '$PBS_O_WORKDIR/'
- MIN_LENGTH_DEFAULT = 40
- WALLTIME = '100:00:00'
- QUEUE = 'default'
-
- TMP_CMD_FILE_SUFFIX = '_QSUB'
-
- HMM = 'HMM'
- RSL = 'RSL'
-
- OPTION_OPEN = '%['
- OPTION_CLOSE = ']%'
-
- WAIT = 1.0
-
- NL = Constants::LINE_DELIMITER
-
- def run
-
- Util.print_program_information( PRG_NAME,
- PRG_VERSION,
- PRG_DESC,
- PRG_DATE,
- COPYRIGHT,
- CONTACT,
- WWW,
- STDOUT )
-
- begin
- cla = CommandLineArguments.new( ARGV )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
- end
-
- allowed_opts = Array.new
- allowed_opts.push( USE_JOB_SUBMISSION_SYSTEM_OPTION )
-
- disallowed = cla.validate_allowed_options_as_str( allowed_opts )
- if ( disallowed.length > 0 )
- Util.fatal_error( PRG_NAME,
- "unknown option(s): " + disallowed,
- STDOUT )
- end
-
- if File.exists?( LOG_FILE )
- puts( '[' + PRG_NAME + '] > log file [' + LOG_FILE + '] already exists' )
- exit( -1 )
- end
-
- if !File.exists?( TEMPLATE_FILE )
- puts( '[' + PRG_NAME + '] > template file [' + TEMPLATE_FILE + '] not found' )
- exit( -1 )
- end
-
- use_job_submission_system = false
- if cla.is_option_set?( USE_JOB_SUBMISSION_SYSTEM_OPTION )
- use_job_submission_system = true
+ class PhylogenyFactory
+
+ PRG_NAME = "phylogeny_factory"
+ PRG_DATE = "130402"
+ PRG_DESC = "automated phylogeny reconstruction using queing system"
+ PRG_VERSION = "1.002"
+ COPYRIGHT = "2013 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ USE_JOB_SUBMISSION_SYSTEM_OPTION = 's'
+ LOG_FILE = '00_phylogeny_factory.log'
+ TEMPLATE_FILE = '00_phylogeny_factory.template'
+ PBS_O_WORKDIR = '$PBS_O_WORKDIR/'
+ MIN_LENGTH_DEFAULT = 50
+ PFAM_HHMS = "/home/czmasek/DATA/PFAM/PFAM260X/PFAM_A_HMMs/"
+ WALLTIME = '100:00:00'
+ QUEUE = 'default'
+
+ TMP_CMD_FILE_SUFFIX = '_QSUB'
+
+ RSL = 'RSL'
+ HMM = 'HMM'
+
+ OPTION_OPEN = '%['
+ OPTION_CLOSE = ']%'
+
+ WAIT = 1.0
+
+ NL = Constants::LINE_DELIMITER
+
+ def run
+
+ Util.print_program_information( PRG_NAME,
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ COPYRIGHT,
+ CONTACT,
+ WWW,
+ STDOUT )
+
+ begin
+ cla = CommandLineArguments.new( ARGV )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+
+ allowed_opts = Array.new
+ allowed_opts.push( USE_JOB_SUBMISSION_SYSTEM_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
+
+ if File.exists?( LOG_FILE )
+ puts( '[' + PRG_NAME + '] > log file [' + LOG_FILE + '] already exists' )
+ exit( -1 )
+ end
+
+ if !File.exists?( TEMPLATE_FILE )
+ puts( '[' + PRG_NAME + '] > template file [' + TEMPLATE_FILE + '] not found' )
+ exit( -1 )
+ end
+
+ use_job_submission_system = false
+ if cla.is_option_set?( USE_JOB_SUBMISSION_SYSTEM_OPTION )
+ use_job_submission_system = true
+ end
+
+ log = String.new
+
+ now = DateTime.now
+ log << "Program : " + PRG_NAME + NL
+ log << "Version : " + PRG_VERSION + NL
+ log << "Program date: " + PRG_DATE + NL + NL
+ log << "Date/time : " + now.to_s + NL
+ log << "Directory : " + Dir.getwd + NL + NL
+
+ puts( '[' + PRG_NAME + '] > reading ' + TEMPLATE_FILE )
+
+ paths = Hash.new # path placeholder -> full path
+ min_lengths = Hash.new # alignment id -> minimal length
+ options = Hash.new # option placeholder -> option
+ # ids = Set.new
+
+ commands = Array.new
+
+ log << "////////////////////////////////////////////////////////////////// #{NL}"
+ log << "Template file [" + TEMPLATE_FILE + "]:#{NL}"
+
+ command = String.new
+
+ open( TEMPLATE_FILE ).each { | line |
+ log << line
+ if ( line =~ /^#/ )
+ elsif ( line =~ /^\$\s*(\S+)\s*=\s*(\S+)/ )
+ paths[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > paths : ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^%\s*#{RSL}\s*(\S+)\s*=\s*(\S+)/ )
+ min_lengths[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > min lengths: ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ )
+ options[ $1 ] = $2
+ puts( '[' + PRG_NAME + '] > options : ' + $1 + ' => ' + $2 )
+
+ elsif ( line =~ /^>\s*(.+)/ )
+ command = command + $1 + ";#{NL}"
+
+ elsif ( line =~ /^-/ )
+ commands << prepare( command, paths )
+ command = String.new
+ end
+ }
+ log << "\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ #{NL}#{NL}"
+
+ files = Dir.entries( "." )
+
+ files.each { | file |
+ if ( !File.directory?( file ) &&
+ file !~ /^\./ &&
+ file !~ /#{TEMPLATE_FILE}/ &&
+ file !~ /.bck$/ &&
+ file !~ /.log$/ &&
+ file !~ /nohup/ &&
+ file !~ /^00/ )
+ aln_name = file.to_str
+ id = get_id( aln_name )
+ #if !ids.include?( id )
+ # ids.add( id )
+ #end
+ if id != nil && id.length > 0
+ puts( '[' + PRG_NAME + '] > file [id]: ' + aln_name + ' [' + id + ']' )
+ else
+ puts( '[' + PRG_NAME + '] > file [id]: ' + aln_name + ' [WARNING: could not get id!]' )
+ end
+ commands.each do | cmd |
+ cmd = subst_hmm( cmd, id )
+ cmd = subst_min_length( cmd, id, min_lengths )
+ cmd = subst_options( cmd, options )
+ if use_job_submission_system
+ cmd = subst_aln_name( cmd, PBS_O_WORKDIR + aln_name )
+ else
+ cmd = subst_aln_name( cmd, aln_name )
end
- log = String.new
-
- now = DateTime.now
- log << "Program : " + PRG_NAME + NL
- log << "Version : " + PRG_VERSION + NL
- log << "Program date: " + PRG_DATE + NL + NL
- log << "Date/time : " + now.to_s + NL
- log << "Directory : " + Dir.getwd + NL + NL
-
- puts( '[' + PRG_NAME + '] > reading ' + TEMPLATE_FILE )
-
- paths = Hash.new # path placeholder -> full path
- min_lengths = Hash.new # alignment id -> minimal length
- hmms = Hash.new # alignment id -> hmm
- options = Hash.new # option placeholder -> option
- ids = Set.new
-
- commands = Array.new
-
- log << "////////////////////////////////////////////////////////////////// #{NL}"
- log << "Template file [" + TEMPLATE_FILE + "]:#{NL}"
-
- command = String.new
-
- open( TEMPLATE_FILE ).each { | line |
- log << line
- if ( line =~ /^#/ )
- elsif ( line =~ /^\$\s*(\S+)\s*=\s*(\S+)/ )
- paths[ $1 ] = $2
- puts( '[' + PRG_NAME + '] > paths : ' + $1 + ' => ' + $2 )
-
- elsif ( line =~ /^%\s*#{HMM}\s*(\S+)\s*=\s*(\S+)/ )
- hmms[ $1 ] = $2
- puts( '[' + PRG_NAME + '] > hmms : ' + $1 + ' => ' + $2 )
-
- elsif ( line =~ /^%\s*#{RSL}\s*(\S+)\s*=\s*(\S+)/ )
- min_lengths[ $1 ] = $2
- puts( '[' + PRG_NAME + '] > min lengths: ' + $1 + ' => ' + $2 )
-
- elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ )
- options[ $1 ] = $2
- puts( '[' + PRG_NAME + '] > options : ' + $1 + ' => ' + $2 )
-
- elsif ( line =~ /^>\s*(.+)/ )
- command = command + $1 + ";#{NL}"
-
- elsif ( line =~ /^-/ )
- commands << prepare( command, paths )
- command = String.new
- end
- }
- log << "\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ #{NL}#{NL}"
-
- files = Dir.entries( "." )
-
- files.each { | file |
- if ( !File.directory?( file ) &&
- file !~ /^\./ &&
- file !~ /#{TEMPLATE_FILE}/ &&
- file !~ /.bck$/ &&
- file !~ /.log$/ &&
- file !~ /nohup/ &&
- file !~ /^00/ )
- aln_name = file.to_str
- id = get_id( aln_name )
- if !ids.include?( id )
- ids.add( id )
- end
- puts( '[' + PRG_NAME + '] > file [id] : ' + aln_name + ' [' + id + ']' )
- commands.each do | cmd |
-
- cmd = subst_hmm( cmd, aln_name, hmms )
- cmd = subst_min_length( cmd, aln_name, min_lengths )
- cmd = subst_options( cmd, options )
- if use_job_submission_system
- cmd = subst_aln_name( cmd, PBS_O_WORKDIR + aln_name )
- else
- cmd = subst_aln_name( cmd, aln_name )
- end
-
- if ( cmd =~ /%/ )
- cmd =~ /(%.*?%)/
- problem = $1
- puts( '[' + PRG_NAME + '] > WARNING : [' + id + '] command still contains placeholder: ' + problem )
- log << "WARNING: command still contains placeholder: " + cmd + NL
- else
- tmp_cmd_file = file.to_str[ 0..4 ] + TMP_CMD_FILE_SUFFIX
- if ( File.exists?( tmp_cmd_file ) )
- File.delete( tmp_cmd_file )
- end
- if use_job_submission_system
- open( tmp_cmd_file, 'w' ) do |f|
- f.write( cmd )
- end
- end
-
- log << cmd + NL
-
- if use_job_submission_system
- IO.popen( 'qsub -q ' + QUEUE + ' -l walltime=' + WALLTIME + ' ' + tmp_cmd_file , 'r+' ) do | pipe |
- pipe.close_write
- end
- else
- spawn( 'nohup ' + cmd + ' &', STDERR => "/dev/null" )
- end
-
- sleep( WAIT )
- if ( File.exists?( tmp_cmd_file ) )
- File.delete( tmp_cmd_file )
- end
- end
- end
+ if ( cmd =~ /%/ )
+ cmd =~ /(%.*?%)/
+ problem = $1
+ puts( '[' + PRG_NAME + '] > WARNING : [' + aln_name + '] command still contains placeholder: ' + problem )
+ log << "WARNING: command still contains placeholder: " + cmd + NL
+ else
+ tmp_cmd_file = file.to_str[ 0..4 ] + TMP_CMD_FILE_SUFFIX
+ if ( File.exists?( tmp_cmd_file ) )
+ File.delete( tmp_cmd_file )
+ end
+ if use_job_submission_system
+ open( tmp_cmd_file, 'w' ) do |f|
+ f.write( cmd )
end
- }
+ end
- open( LOG_FILE, 'w' ) do | f |
- f.write( log )
- end
-
- puts()
- puts( '[' + PRG_NAME + '] > OK' )
- puts()
-
- end # def run
-
- def prepare( command, paths )
- paths.each_pair{ | name, full |
- command = command.gsub( name, full )
- }
- command
- end
+ log << cmd + NL
- def subst_options( command, options )
- opt_placeholders = command.scan( /%\[\S+\]%/ )
- opt_placeholders.each { | opt_placeholder |
- opt_placeholder = opt_placeholder.gsub( OPTION_OPEN , '' )
- opt_placeholder = opt_placeholder.gsub( OPTION_CLOSE, '' )
- opt_value = options[ opt_placeholder ]
- if ( opt_value != nil && opt_value.size > 0 )
- command = command.gsub( OPTION_OPEN + opt_placeholder + OPTION_CLOSE, opt_value )
+ if use_job_submission_system
+ IO.popen( 'qsub -q ' + QUEUE + ' -l walltime=' + WALLTIME + ' ' + tmp_cmd_file , 'r+' ) do | pipe |
+ pipe.close_write
end
- }
- command
- end
-
- def subst_aln_name( command, aln_name )
- command = command.gsub( '$', aln_name )
- command
- end
-
- def subst_hmm( command, aln_name, hmms )
- id = get_id( aln_name )
- hmm = hmms[ id ]
- if ( hmm != nil && hmm.size > 0 )
- command = command.gsub( OPTION_OPEN + HMM + OPTION_CLOSE, hmm )
- end
- command
- end
-
- def subst_min_length( command, aln_name, min_lengths )
- id = get_id( aln_name )
- min_length = min_lengths[ id ]
- if ( min_length != nil && min_length.size > 0 )
- command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, min_length )
- else
- command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, MIN_LENGTH_DEFAULT.to_s )
+ else
+ spawn( 'nohup ' + cmd + ' &', STDERR => "/dev/null" )
+ end
+
+ sleep( WAIT )
+ if ( File.exists?( tmp_cmd_file ) )
+ File.delete( tmp_cmd_file )
+ end
end
- command
+ end
end
-
- def get_id( aln_name )
- aln_name =~ /^([^_]+)/
- $1
+ }
+
+ open( LOG_FILE, 'w' ) do | f |
+ f.write( log )
+ end
+
+ puts()
+ puts( '[' + PRG_NAME + '] > OK' )
+ puts()
+
+ end # def run
+
+ def prepare( command, paths )
+ paths.each_pair{ | name, full |
+ command = command.gsub( name, full )
+ }
+ command
+ end
+
+ def subst_options( command, options )
+ opt_placeholders = command.scan( /%\[\S+\]%/ )
+ opt_placeholders.each { | opt_placeholder |
+ opt_placeholder = opt_placeholder.gsub( OPTION_OPEN , '' )
+ opt_placeholder = opt_placeholder.gsub( OPTION_CLOSE, '' )
+ opt_value = options[ opt_placeholder ]
+ if ( opt_value != nil && opt_value.size > 0 )
+ command = command.gsub( OPTION_OPEN + opt_placeholder + OPTION_CLOSE, opt_value )
end
-
- end # class PhylogenyFactory
+ }
+ command
+ end
+
+ def subst_aln_name( command, aln_name )
+ command = command.gsub( '$', aln_name )
+ command
+ end
+
+ def subst_hmm( command, id )
+ if id != nil && id.length > 0
+ hmm = PFAM_HHMS + id + ".hmm"
+ command = command.gsub( OPTION_OPEN + HMM + OPTION_CLOSE, hmm )
+ end
+ command
+ end
+
+ def subst_min_length( command, id, min_lengths )
+ min_length = nil
+ if id != nil && id.length > 0
+ min_length = min_lengths[ id ]
+ end
+ if min_length != nil && min_length.size > 0
+ command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, min_length )
+ else
+ command = command.gsub( OPTION_OPEN + RSL + OPTION_CLOSE, MIN_LENGTH_DEFAULT.to_s )
+ end
+ command
+ end
+
+ def get_id( aln_name )
+ id = nil
+ if aln_name.include? "__"
+ id = aln_name[ 0, aln_name.index( "__" ) ]
+ end
+ id
+ end
+
+ end # class PhylogenyFactory
end # module Evoruby
git://source.jalview.org / jalview.git / blobdiff