X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogeny_factory.rb;h=18d396e25eedef4828a497d341de057643ff0374;hb=73a72373e1e807ea755fbeb072ad979034e6d05a;hp=cb72a02bf2d73c984a957b577f5c059104e57c4d;hpb=3beb7e9f04fb86e3dbbae1c89b4100ec31e78ce0;p=jalview.git diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb index cb72a02..18d396e 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb @@ -18,19 +18,20 @@ module Evoruby class PhylogenyFactory PRG_NAME = "phylogeny_factory" - PRG_DATE = "130402" + PRG_DATE = "1301111" PRG_DESC = "automated phylogeny reconstruction using queing system" - PRG_VERSION = "1.002" + 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 = 50 - PFAM_HHMS = "/home/czmasek/DATA/PFAM/PFAM260X/PFAM_A_HMMs/" + MIN_LENGTH_DEFAULT = 40 + PFAM_HHMS = "/home/czmasek/DATA/PFAM/PFAM270X/PFAM_A_HMMs/" WALLTIME = '100:00:00' QUEUE = 'default' @@ -38,6 +39,7 @@ module Evoruby RSL = 'RSL' HMM = 'HMM' + PHYLO_OPT = 'PHYLO_OPT' OPTION_OPEN = '%[' OPTION_CLOSE = ']%' @@ -65,6 +67,7 @@ module Evoruby 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 ) @@ -88,12 +91,25 @@ module Evoruby 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 @@ -102,7 +118,6 @@ module Evoruby 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 @@ -123,8 +138,13 @@ module Evoruby puts( '[' + PRG_NAME + '] > min lengths: ' + $1 + ' => ' + $2 ) elsif ( line =~ /^%\s*(\S+)\s*=\s*(\S+)/ ) - options[ $1 ] = $2 - puts( '[' + PRG_NAME + '] > options : ' + $1 + ' => ' + $2 ) + 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}" @@ -243,6 +263,19 @@ module Evoruby 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 @@ -297,45 +330,86 @@ $ PHYLO_PL=/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/archive/perl/ph % RSL Y_phosphatase3=50 % RSL Y_phosphatase3C=40 -% PHYLO_OPT=-B100q@1r4j2IGS21X +% PHYLO_OPT=B100q@1r4j2IGS21X % TMP_DIR = /home/czmasek/tmp/ > KALIGN $ > $_kalign -> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_kalign $_kalign_05_%[RSL]%.aln +> 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]% - +> 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]% +- + + > HMMALIGN --amino --trim --outformat Pfam -o $_hmmalign %[HMM]% $ > /dev/null -> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_hmmalign $_hmmalign_05_%[RSL]%.aln +> 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]% - +> 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]% +- + + > MAFFT --maxiterate 1000 --localpair $ > $_mafft -> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_mafft $_mafft_05_%[RSL]%.aln +> 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]% - +> 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]% +- + + > MUSCLE -maxiters 1000 -maxtrees 100 -in $ -out $_muscle -> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_muscle $_muscle_05_%[RSL]%.aln -> PHYLO_PL %[PHYLO_OPT]% $_muscle_05_%[RSL]%.aln $_muscle_05_%[RSL]% %[TMP_DIR]% +> 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]% - +> 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]% +- + + > CLUSTALO --full --full-iter --iter=5 -i $ -o $_clustalo -> MSA_PRO -o=p -n=10 -rr=0.5 -c -rsl=%[RSL]% $_clustalo $_clustalo_05_%[RSL]%.aln +> 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]% - +> 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]% +- + + > PROBCONS $ > $_probcons -> MSA_PRO -o=p -n=10 -rem_red -rr=0.5 -c -rsl=%[RSL]% $_probcons $_probcons_05_%[RSL]%.aln +> 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 -rem_red -rr=0.5 -c -rsl=%[RSL]% $_dialigntx $_dialigntx_05_%[RSL]%.aln +> 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