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/PFAM260X/"
  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
  24     def run
  25       unless ARGV.length == 4
  26         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
  27       end
  28
  29
  30
  31
  32       input       = ARGV[ 0 ]
  33       hmm         = ARGV[ 1 ]
  34       length      = ARGV[ 2 ].to_i
  35       e_value_exp = ARGV[ 3 ].to_i
  36
  37       hmmscan_option = "--nobias"
  38       e_for_hmmscan = 100
  39
  40       if e_value_exp < 0
  41         error "e-value exponent cannot be negative"
  42       end
  43       if length <= 1
  44         error "length exponent cannot be smaller than or equal to 1"
  45       end
  46
  47       base_name = nil
  48       if input.downcase.end_with?( ".fasta" )
  49         base_name = input[ 0 .. input.length - 7 ]
  50       elsif input.downcase.end_with?( ".fsa" )
  51         base_name = input[ 0 .. input.length - 5 ]
  52       else
  53         base_name = input
  54       end
  55
  56       puts "1. hmmscan:"
  57       cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  58       run_command( cmd )
  59       puts
  60
  61       puts "2. hmmscan to simple domain table:"
  62       cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
  63       run_command( cmd )
  64       puts
  65
  66       puts "3. domain table to forester format:"
  67       cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
  68       run_command( cmd )
  69       puts
  70
  71       puts "4. dsx:"
  72       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}_e#{e_value_exp.to_s}_#{length}"
  73       run_command( cmd )
  74       puts
  75
  76     end
  77
  78     def run_command( cmd )
  79       puts cmd
  80       `#{cmd}`
  81     end
  82
  83     def error msg
  84       puts
  85       puts msg
  86       puts
  87       exit
  88     end
  89
  90   end
  91
  92   p = RunPhyloPipeline.new()
  93
  94   p.run()
  95
  96 end
  97
  98
  99