forester/ruby/evoruby/exe/run_phylo_pipeline.rb

   1 #!/usr/local/bin/ruby -w
   2 #
   3 # = run_phylo_pipeline
   4 #
   5 # Copyright::  Copyright (C) 2010 Christian M. Zmasek
   6 # License::    GNU Lesser General Public License (LGPL)
   7 #
   8 # $Id: run_phylo_pipeline.rb,v 1.15 2010/10/09 02:35:42 cmzmasek Exp $
   9 #
  10 #
  11
  12
  13 #  hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm <BACTH_CHIPI>.fasta
  14
  15 #  hsp <BACTH_CHIPI>_hmmscan_250_10 <BACTH_CHIPI>_hmmscan_250_10_domain_table
  16
  17 #  d2f -e=10 <BACTH_CHIPI>_hmmscan_250_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_250_10.dff
  18
  19 # hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD  <~/DATA/PFAM/PFAM250/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
  20
  21 # dsx -dd -e=<1e-2> -l=<200> <BACTH_CHIPI>.hmmsearch_SusD <BACTH_CHIPI>.fasta BACTH_CHIPI_e2_200
  22
  23
  24 module Evoruby
  25
  26   class RunPhyloPipeline
  27
  28     def run
  29       unless ARGV.length == 4
  30         puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]"
  31         exit
  32       end
  33
  34       pfam      = "/home/czmasek/DATA/PFAM/PFAM260/"
  35       hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
  36       hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
  37       hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
  38       d2f       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
  39       dsx       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
  40
  41       base_name   = ARGV[ 0 ]
  42       hmm         = ARGV[ 1 ]
  43       length      = ARGV[ 2 ]
  44       e_value_exp = ARGV[ 3 ]
  45       do_domain_combination_analysis = true
  46
  47       if do_domain_combination_analysis
  48
  49         cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{pfam}Pfam-A.hmm #{base_name}.fasta"
  50         run_command( cmd )
  51
  52         cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
  53         run_command( cmd )
  54
  55         cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_10.dff"
  56         run_command( cmd )
  57
  58       end
  59
  60       cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  #{pfam}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
  61       run_command( cmd )
  62
  63       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}"
  64       run_command( cmd )
  65
  66     end
  67
  68     def run_command( cmd )
  69       puts cmd
  70       `#{cmd}`
  71     end
  72
  73   end
  74
  75   p = RunPhyloPipeline.new()
  76
  77   p.run()
  78
  79 end
  80
  81
  82