From a967f526fcc04637849901cd503ffde16bb5248e Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 28 Sep 2012 01:52:24 +0000 Subject: [PATCH] in progress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 57 +++++++++++++++-------- 1 file changed, 38 insertions(+), 19 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index d09655f..3c6d0fe 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -5,35 +5,24 @@ # Copyright:: Copyright (C) 2010 Christian M. Zmasek # License:: GNU Lesser General Public License (LGPL) # -# $Id: run_phylo_pipeline.rb,v 1.15 2010/10/09 02:35:42 cmzmasek Exp $ +# $Id Exp $ # # -# hmmscan --nobias --domtblout _hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm .fasta - -# hsp _hmmscan_250_10 _hmmscan_250_10_domain_table - -# d2f -e=10 _hmmscan_250_10_domain_table .fasta _hmmscan_250_10.dff - -# hmmsearch --nobias -E 1000 --domtblout .hmmsearch_SusD <~/DATA/PFAM/PFAM250/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta +module Evoruby -# dsx -dd -e=<1e-2> -l=<200> .hmmsearch_SusD .fasta BACTH_CHIPI_e2_200 + class RunPhyloPipeline + PFAM = "/home/czmasek/DATA/PFAM/PFAM260X/" -module Evoruby - class RunPhyloPipeline def run unless ARGV.length == 4 - puts - puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]" - puts - exit + error "arguments are: " end - pfam = "/home/czmasek/DATA/PFAM/PFAM260X/" 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" @@ -46,24 +35,47 @@ module Evoruby e_value_exp = ARGV[ 3 ] do_domain_combination_analysis = true + if e_value_exp < 0 + error "e-value exponent cannot be negative" + end + if length <= 1 + 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 ] + end + if do_domain_combination_analysis - cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{pfam}Pfam-A.hmm #{base_name}.fasta" + puts "hmmscan:" + cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{base_name}.fasta" run_command( cmd ) + puts + puts "hmmscan to simple domain table:" cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table" run_command( cmd ) + 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" run_command( cmd ) + puts end - cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{pfam}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" + puts "hmmsearch:" + cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta" run_command( cmd ) + puts - 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}" + 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}" run_command( cmd ) + puts end @@ -72,6 +84,13 @@ module Evoruby `#{cmd}` end + def error msg + puts + puts msg + puts + exit + end + end p = RunPhyloPipeline.new() -- 1.7.10.2