From 93b9f80ae6a390a4cf014e9262c1e4a2f7ff24db Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 01:21:31 +0000 Subject: [PATCH] in progress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index 45142f0..a36f56a 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -31,6 +31,7 @@ module Evoruby exit end + pfam = "/home/czmasek/DATA/PFAM/PFAM260/" 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" @@ -45,18 +46,18 @@ module Evoruby if do_domain_combination_analysis - cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm #{base_name}.fasta" + cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{pfam}Pfam-A.hmm #{base_name}.fasta" run_command( cmd ) - cmd = "#{hsp} #{base_name}_hmmscan_250_10 #{base_name}_hmmscan_250_10_domain_table" + cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table" run_command( cmd ) - cmd = "#{d2f} -e=10 #{base_name}_hmmscan_250_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_250_10.dff" + cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_10.dff" run_command( cmd ) end - cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM250/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" + cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{pfam}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}_#{hmm}_e#{e_value_exp.to_s}_#{length}" -- 1.7.10.2