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 Exp $
   9 #
  10 #
  11
  12
  13 module Evoruby
  14
  15   class RunPhyloPipeline
  16
  17     PFAM      = "/home/czmasek/DATA/PFAM/PFAM270X/"
  18     HMMSCAN  = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
  19     HSP       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
  20     D2F       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
  21     DSX       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
  22
  23     def run
  24       unless ARGV.length >= 4 && ARGV.length <= 6
  25         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> " +
  26          "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]"
  27       end
  28
  29       input       = ARGV[ 0 ]
  30       hmm         = ARGV[ 1 ]
  31       length      = ARGV[ 2 ].to_i
  32       e_value_exp = ARGV[ 3 ].to_i
  33
  34       e_for_hmmscan = 20
  35       hmmscan_option = "--nobias"
  36
  37       if ARGV.length == 6
  38         hmmscan_option = ARGV[ 5 ]
  39       end
  40       if ARGV.length == 5 || ARGV.length == 6
  41         e_for_hmmscan = ARGV[ 4 ].to_i
  42       end
  43
  44       if e_value_exp < 0
  45         error "E-value exponent for domain extraction cannot be negative"
  46       end
  47       if length <= 1
  48         error "length cannot be smaller than or equal to 1"
  49       end
  50       if e_for_hmmscan < 1
  51         error "E-value for hmmscan cannot be smaller than 1"
  52       end
  53
  54       base_name = get_base_name input
  55
  56       puts
  57       puts "1. hmmscan:"
  58       cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  59       run_command( cmd )
  60       puts
  61
  62       puts "2. hmmscan to simple domain table:"
  63       cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
  64       run_command( cmd )
  65       puts
  66
  67       puts "3. domain table to forester format:"
  68       cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
  69       run_command( cmd )
  70       puts
  71
  72       puts "4. dsx:"
  73       cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}__#{hmm}__ee#{e_value_exp.to_s}_#{length}"
  74       run_command( cmd )
  75       puts
  76
  77     end
  78
  79     def run_command cmd
  80       puts cmd
  81       `#{cmd}`
  82     end
  83
  84     def get_base_name n
  85       if n.downcase.end_with?( "_ni.fasta" )
  86         n[ 0 .. n.length - 10 ]
  87       elsif n.downcase.end_with?( ".fasta" )
  88         n[ 0 .. n.length - 7 ]
  89       elsif n.downcase.end_with?( "_ni.fsa" )
  90         n[ 0 .. n.length - 8 ]
  91       elsif n.downcase.end_with?( ".fsa" )
  92         n[ 0 .. n.length - 5 ]
  93       else
  94         n
  95       end
  96     end
  97
  98     def error msg
  99       puts
 100       puts msg
 101       puts
 102       exit
 103     end
 104
 105   end
 106
 107   p = RunPhyloPipeline.new()
 108
 109   p.run()
 110
 111 end
 112
 113
 114