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 = '$PBS_O_WORKDIR/'
- MIN_LENGTH_DEFAULT = 40
- WALLTIME = '100:00:00'
- QUEUE = 'default'
-
- TMP_CMD_FILE_SUFFIX = '_QSUB'
-
- HMM = 'HMM'
- RSL = 'RSL'
-
- OPTION_OPEN = '%['
- OPTION_CLOSE = ']%'
-
- WAIT = 1.0
-
- NL = Constants::LINE_DELIMITER
-
- def run
-
- Util.print_program_information( PRG_NAME,
- PRG_VERSION,
- PRG_DESC,
- PRG_DATE,
- COPYRIGHT,
- CONTACT,
- WWW,
- STDOUT )
-
- begin
- cla = CommandLineArguments.new( ARGV )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ class PhylogenyFactory
+
+ PRG_NAME = "phylogeny_factory"
+ PRG_DATE = "1301111"
+ PRG_DESC = "automated phylogeny reconstruction using queing system"
+ PRG_VERSION = "1.100"
+ COPYRIGHT = "2013 Christian M Zmasek"
+ CONTACT = "phylosoft@gmail.com"
+ WWW = "www.phylosoft.org"
+
+ USE_JOB_SUBMISSION_SYSTEM_OPTION = 's'
+ BS_OPTION = 'b'
+ LOG_FILE = '00_phylogeny_factory.log'
+ TEMPLATE_FILE = '00_phylogeny_factory.template'
+ PBS_O_WORKDIR = '$PBS_O_WORKDIR/'
+ MIN_LENGTH_DEFAULT = 40
+ PFAM_HHMS = "/home/czmasek/DATA/PFAM/PFAM270X/PFAM_A_HMMs/"
+ WALLTIME = '100:00:00'
+ QUEUE = 'default'
+
+ TMP_CMD_FILE_SUFFIX = '_QSUB'
+
+ RSL = 'RSL'
+ HMM = 'HMM'
+ PHYLO_OPT = 'PHYLO_OPT'
+
+ 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 )
+ allowed_opts.push( BS_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
+
+ bootstraps = 1
+ if cla.is_option_set?( BS_OPTION )
+ bootstraps = cla.get_option_value_as_int( BS_OPTION )
+ end
+ if bootstraps < 0
+ puts( '[' + PRG_NAME + '] > negative bootstrap value' )
+ exit( -1 )
+ end
+ if bootstraps == 0
+ bootstraps = 1
+ 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 << "Bootstraps : " + bootstraps.to_s + 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
+
+ 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+)/ )
+ key = $1
+ value = $2
+ if key == PHYLO_OPT
+ value = update_phylo_pl_options( value, bootstraps )
+ end
+ options[ key ] = value
+ puts( '[' + PRG_NAME + '] > options : ' + key + ' => ' + value )
+
+ 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 id != nil && id.length > 0
+ puts
+ puts( '[' + PRG_NAME + '] > file [id] : ' + aln_name + ' [' + id + ']' )
+ else
+ puts
+ 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
- allowed_opts = Array.new
- allowed_opts.push( USE_JOB_SUBMISSION_SYSTEM_OPTION )
+ if ( cmd =~ /%/ )
+ cmd =~ /(%.*?%)/
+ problem = $1
+ puts( '[' + PRG_NAME + '] > WARNING : 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
- disallowed = cla.validate_allowed_options_as_str( allowed_opts )
- if ( disallowed.length > 0 )
- Util.fatal_error( PRG_NAME,
- "unknown option(s): " + disallowed,
- STDOUT )
- end
+ log << cmd + NL
- if File.exists?( LOG_FILE )
- puts( '[' + PRG_NAME + '] > log file [' + LOG_FILE + '] already exists' )
- exit( -1 )
+ 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
+ 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
+
+ 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
+ }
+ 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 update_phylo_pl_options( phylo_pl_options, bootstraps )
+ #opts = phylo_pl_options
+ puts
+ puts "opts: " + phylo_pl_options
+ unless phylo_pl_options =~ /B\d/
+ phylo_pl_options = 'B' + bootstraps.to_s + phylo_pl_options
+ end
+ phylo_pl_options = '-' + phylo_pl_options
+ puts
+ puts "new opts: " + phylo_pl_options
+ phylo_pl_options
+ 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 )
+ if aln_name =~ /_{2}(.+)_{2}/
+ return $1
+ end
+ nil
+ end
+
+ end # class PhylogenyFactory
- if !File.exists?( TEMPLATE_FILE )
- puts( '[' + PRG_NAME + '] > template file [' + TEMPLATE_FILE + '] not found' )
- exit( -1 )
- end
+end # module Evoruby
- use_job_submission_system = false
- if cla.is_option_set?( USE_JOB_SUBMISSION_SYSTEM_OPTION )
- use_job_submission_system = true
- end
- log = String.new
+=begin
- now = DateTime.now
- log << "Program : " + PRG_NAME + NL
- log << "Version : " + PRG_VERSION + NL
- log << "Program date: " + PRG_DATE + NL + NL
- log << "Date/time : " + now.to_s + NL
- log << "Directory : " + Dir.getwd + NL + NL
+# Name convention if alignment specific parameters
+# are to be used:
+# the substring between the first two double underscores is a
+# unique identifier and needs to match the identifiers
+# in '% <parameter-type> <unique-id>=<value>' statements
+# Example:
+# alignment name : 'x__bcl2__e1'
+# parameter statments: '% RSL bcl2=60'
+$ PROBCONS=/home/czmasek/SOFTWARE/PROBCONS/probcons_v1_12/probcons
+$ DIALIGN_TX=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.2/source/dialign-tx
+$ DIALIGN_CONF=/home/czmasek/SOFTWARE/DIALIGNTX/DIALIGN-TX_1.0.2/conf
+$ MAFFT=/home/czmasek/SOFTWARE/MAFFT/mafft-7.017-without-extensions/scripts/mafft
+$ MUSCLE=/home/czmasek/SOFTWARE/MUSCLE/muscle3.8.31/src/muscle
+$ CLUSTALO=/home/czmasek/SOFTWARE/CLUSTAL_OMEGA/clustal-omega-1.1.0/src/clustalo
+$ KALIGN=/home/czmasek/SOFTWARE/KALIGN/kalign203/kalign
+$ HMMALIGN=/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmalign
+$ MSA_PRO=/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/msa_pro.rb
+$ PHYLO_PL=/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/archive/perl/phylo_pl.pl
- 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
+% RSL Hormone_recep=60
+%
+% RSL Y_phosphatase=100
+% RSL Y_phosphatase2=75
+% RSL Y_phosphatase3=50
+% RSL Y_phosphatase3C=40
- commands = Array.new
+% PHYLO_OPT=B100q@1r4j2IGS21X
- log << "////////////////////////////////////////////////////////////////// #{NL}"
- log << "Template file [" + TEMPLATE_FILE + "]:#{NL}"
+% TMP_DIR = /home/czmasek/tmp/
- 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 )
+> KALIGN $ > $_kalign
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_kalign_05_%[RSL]%.aln $_kalign_05_%[RSL]% %[TMP_DIR]%
+-
- elsif ( line =~ /^%\s*#{HMM}\s*(\S+)\s*=\s*(\S+)/ )
- hmms[ $1 ] = $2
- puts( '[' + PRG_NAME + '] > hmms : ' + $1 + ' => ' + $2 )
+> KALIGN $ > $_kalign_
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_kalign_ $_kalign_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_kalign_09_%[RSL]%.aln $_kalign_09_%[RSL]% %[TMP_DIR]%
+-
- 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 )
+> HMMALIGN --amino --trim --outformat Pfam -o $_hmmalign %[HMM]% $ > /dev/null
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_05_%[RSL]%.aln $_hmmalign_05_%[RSL]% %[TMP_DIR]%
+-
- elsif ( line =~ /^>\s*(.+)/ )
- command = command + $1 + ";#{NL}"
+> HMMALIGN --amino --trim --outformat Pfam -o $_hmmalign_ %[HMM]% $ > /dev/null
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_hmmalign_ $_hmmalign_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_09_%[RSL]%.aln $_hmmalign_09_%[RSL]% %[TMP_DIR]%
+-
- elsif ( line =~ /^-/ )
- commands << prepare( command, paths )
- command = String.new
- end
- }
- log << "\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ #{NL}#{NL}"
-
- files = Dir.entries( "." )
-
- files.each { | file |
- if ( !File.directory?( file ) &&
- file !~ /^\./ &&
- file !~ /#{TEMPLATE_FILE}/ &&
- file !~ /.bck$/ &&
- 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
- end
- }
- open( LOG_FILE, 'w' ) do | f |
- f.write( log )
- end
+> MAFFT --maxiterate 1000 --localpair $ > $_mafft
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_mafft_05_%[RSL]%.aln $_mafft_05_%[RSL]% %[TMP_DIR]%
+-
- puts()
- puts( '[' + PRG_NAME + '] > OK' )
- puts()
+> MAFFT --maxiterate 1000 --localpair $ > $_mafft_
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_mafft_ $_mafft_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_mafft_09_%[RSL]%.aln $_mafft_09_%[RSL]% %[TMP_DIR]%
+-
- end # def run
- def prepare( command, paths )
- paths.each_pair{ | name, full |
- command = command.gsub( name, full )
- }
- command
- end
+> MUSCLE -maxiters 1000 -maxtrees 100 -in $ -out $_muscle
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]%
+-
- 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
- }
- command
- end
+> MUSCLE -maxiters 1000 -maxtrees 100 -in $ -out $_muscle_
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_muscle_ $_muscle_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_muscle_09_%[RSL]%.aln $_muscle_09_%[RSL]% %[TMP_DIR]%
+-
- def subst_aln_name( command, aln_name )
- command = command.gsub( '$', 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
+> CLUSTALO --full --full-iter --iter=5 -i $ -o $_clustalo
+> MSA_PRO -o=p -n=10 -d -rr=0.5 -c -rsl=%[RSL]% $_clustalo $_clustalo_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_clustalo_05_%[RSL]%.aln $_clustalo_05_%[RSL]% %[TMP_DIR]%
+-
- 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 )
- end
- command
- end
+> CLUSTALO --full --full-iter --iter=5 -i $ -o $_clustalo_
+> MSA_PRO -o=p -n=10 -d -rr=0.9 -c -rsl=%[RSL]% $_clustalo_ $_clustalo_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_clustalo_09_%[RSL]%.aln $_clustalo_09_%[RSL]% %[TMP_DIR]%
+-
- def get_id( aln_name )
- aln_name =~ /^([^_]+)/
- $1
- end
- end # class PhylogenyFactory
+> PROBCONS $ > $_probcons
+> MSA_PRO -o=p -n=10 -d -rem_red -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_probcons_05_%[RSL]%.aln $_probcons_05_%[RSL]% %[TMP_DIR]%
+-
+
+> PROBCONS $ > $_probcons_
+> MSA_PRO -o=p -n=10 -d -rem_red -rr=0.9 -c -rsl=%[RSL]% $_probcons_ $_probcons_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_probcons_09_%[RSL]%.aln $_probcons_09_%[RSL]% %[TMP_DIR]%
+-
+
+
+> DIALIGN_TX DIALIGN_CONF $ $_dialigntx
+> MSA_PRO -o=p -n=10 -d -rem_red -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_dialigntx_05_%[RSL]%.aln $_dialigntx_05_%[RSL]% %[TMP_DIR]%
+-
+
+> DIALIGN_TX DIALIGN_CONF $ $_dialigntx_
+> MSA_PRO -o=p -n=10 -d -rem_red -rr=0.9 -c -rsl=%[RSL]% $_dialigntx_ $_dialigntx_09_%[RSL]%.aln
+> PHYLO_PL %[PHYLO_OPT]% $_dialigntx_09_%[RSL]%.aln $_dialigntx_09_%[RSL]% %[TMP_DIR]%
+-
+
+=end
-end # module Evoruby
git://source.jalview.org / jalview.git / blobdiff