From aca666756d58f186309fd318c31f26080e59ca32 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Mon, 18 Apr 2011 21:36:55 +0000 Subject: [PATCH] updated to pfam25 --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 26 +++++++++++------------ 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index d68c58b..d59c61c 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -10,13 +10,13 @@ # -# hmmscan --nobias --domtblout _hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm .fasta +# hmmscan --nobias --domtblout _hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm .fasta -# hsp _hmmscan_240_10 _hmmscan_240_10_domain_table +# hsp _hmmscan_250_10 _hmmscan_250_10_domain_table -# d2f -e=10 _hmmscan_240_10_domain_table .fasta _hmmscan_240_10.dff +# d2f -e=10 _hmmscan_250_10_domain_table .fasta _hmmscan_250_10.dff -# hmmsearch --nobias -E 1000 --domtblout .hmmsearch_SusD <~/DATA/PFAM/PFAM240/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta +# hmmsearch --nobias -E 1000 --domtblout .hmmsearch_SusD <~/DATA/PFAM/PFAM250/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta # dsx -dd -e=<1e-2> -l=<200> .hmmsearch_SusD .fasta BACTH_CHIPI_e2_200 @@ -31,11 +31,11 @@ module Evoruby exit end - hmmscan = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmscan" - hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmsearch" - hsp = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/hsp.rb" - d2f = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/d2f.rb" - dsx = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/dsx.rb" + hmmscan = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan" + hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch" + hsp = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb" + d2f = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb" + dsx = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb" base_name = ARGV[ 0 ] hmm = ARGV[ 1 ] @@ -45,18 +45,18 @@ module Evoruby if do_domain_combination_analysis - cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm #{base_name}.fasta" + cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm #{base_name}.fasta" run_command( cmd ) - cmd = "#{hsp} #{base_name}_hmmscan_240_10 #{base_name}_hmmscan_240_10_domain_table" + cmd = "#{hsp} #{base_name}_hmmscan_250_10 #{base_name}_hmmscan_250_10_domain_table" run_command( cmd ) - cmd = "#{d2f} -e=10 #{base_name}_hmmscan_240_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_240_10.dff" + cmd = "#{d2f} -e=10 #{base_name}_hmmscan_250_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_250_10.dff" run_command( cmd ) end - cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM240/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" + cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM250/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" run_command( cmd ) cmd = "#{dsx} -dd -e=1e-#{e_value_exp.to_s} -l=#{length} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_e#{e_value_exp.to_s}_#{length}" -- 1.7.10.2