From 3beb7e9f04fb86e3dbbae1c89b4100ec31e78ce0 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 3 Apr 2013 02:16:39 +0000 Subject: [PATCH] inprogress --- .../ruby/evoruby/lib/evo/tool/phylogeny_factory.rb | 73 ++++++++++++++++++++ 1 file changed, 73 insertions(+) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb index 4832d546..cb72a02 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb @@ -266,3 +266,76 @@ module Evoruby end # class PhylogenyFactory end # module Evoruby + + +=begin + +# 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 '% =' 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 + + +% RSL Hormone_recep=60 +% +% RSL Y_phosphatase=100 +% RSL Y_phosphatase2=75 +% RSL Y_phosphatase3=50 +% RSL Y_phosphatase3C=40 + +% 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 +> PHYLO_PL %[PHYLO_OPT]% $_kalign_05_%[RSL]%.aln $_kalign_05_%[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 +> PHYLO_PL %[PHYLO_OPT]% $_hmmalign_05_%[RSL]%.aln $_hmmalign_05_%[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 +> PHYLO_PL %[PHYLO_OPT]% $_mafft_05_%[RSL]%.aln $_mafft_05_%[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]% +- + +> 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 +> PHYLO_PL %[PHYLO_OPT]% $_clustalo_05_%[RSL]%.aln $_clustalo_05_%[RSL]% %[TMP_DIR]% +- + +> PROBCONS $ > $_probcons +> MSA_PRO -o=p -n=10 -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]% +- + +> DIALIGN_TX DIALIGN_CONF $ $_dialigntx +> MSA_PRO -o=p -n=10 -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]% +- + +=end + -- 1.7.10.2