From e331fb593cd3d803581cd02355f64092836dc3d8 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 01:56:12 +0000 Subject: [PATCH] in progress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index 3c6d0fe..e144552 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -29,7 +29,7 @@ module Evoruby 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 ] + input = ARGV[ 0 ] hmm = ARGV[ 1 ] length = ARGV[ 2 ] e_value_exp = ARGV[ 3 ] @@ -42,16 +42,19 @@ module Evoruby error "length exponent cannot be smaller than or equal to 1" end - if base_name.downcase.end_with?( ".fasta" ) - base_name = base_name[ 0 .. base_name.length - 7 ] - elsif base_name.downcase.end_with?( ".fsa" ) - base_name = base_name[ 0 .. base_name.length - 5 ] + base_name = nil + if input.downcase.end_with?( ".fasta" ) + base_name = input[ 0 .. input.length - 7 ] + elsif input.downcase.end_with?( ".fsa" ) + base_name = input[ 0 .. input.length - 5 ] + else + base_name = input end if do_domain_combination_analysis puts "hmmscan:" - cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{base_name}.fasta" + cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{input}" run_command( cmd ) puts @@ -61,19 +64,19 @@ module Evoruby puts puts "domain table to forester format:" - cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_10.dff" + cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{input} #{base_name}_hmmscan_10.dff" run_command( cmd ) puts end puts "hmmsearch:" - cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" + cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{input}" run_command( cmd ) puts puts "dsx:" - cmd = "#{dsx} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}" + cmd = "#{dsx} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}.hmmsearch_#{hmm} #{input} #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}" run_command( cmd ) puts -- 1.7.10.2