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 && ARGV.length <= 6
  26         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> +
  27         <neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias]"
  28       end
  29
  30       input       = ARGV[ 0 ]
  31       hmm         = ARGV[ 1 ]
  32       length      = ARGV[ 2 ].to_i
  33       e_value_exp = ARGV[ 3 ].to_i
  34
  35       e_for_hmmscan = 20
  36       hmmscan_option = "--nobias"
  37
  38       if ARGV.length == 6
  39         hmmscan_option = ARGV[ 5 ]
  40       end
  41       if ARGV.length == 5 || ARGV.length == 6
  42         e_for_hmmscan = ARGV[ 4 ].to_i
  43       end
  44
  45       if e_value_exp < 0
  46         error "E-value exponent for domain extraction cannot be negative"
  47       end
  48       if length <= 1
  49         error "length cannot be smaller than or equal to 1"
  50       end
  51       if e_for_hmmscan < 1
  52         error "E-value for hmmscan cannot be smaller than 1"
  53       end
  54
  55       base_name = get_base_name input
  56
  57       #base_name = nil
  58       #if input.downcase.end_with?( "_ni.fasta" )
  59       #  base_name = input[ 0 .. input.length - 10 ]
  60       #elsif input.downcase.end_with?( ".fasta" )
  61       #  base_name = input[ 0 .. input.length - 7 ]
  62       #elsif input.downcase.end_with?( "_ni.fsa" )
  63       #  base_name = input[ 0 .. input.length - 8 ]
  64       #elsif input.downcase.end_with?( ".fsa" )
  65       #  base_name = input[ 0 .. input.length - 5 ]
  66       #else
  67       #  base_name = input
  68       #end
  69
  70       puts "1. hmmscan:"
  71       cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  72       run_command( cmd )
  73       puts
  74
  75       puts "2. hmmscan to simple domain table:"
  76       cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
  77       run_command( cmd )
  78       puts
  79
  80       puts "3. domain table to forester format:"
  81       cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
  82       run_command( cmd )
  83       puts
  84
  85       puts "4. dsx:"
  86       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}"
  87       run_command( cmd )
  88       puts
  89
  90     end
  91
  92     def run_command cmd
  93       puts cmd
  94       `#{cmd}`
  95     end
  96
  97     def get_base_name n
  98       if n.downcase.end_with?( "_ni.fasta" )
  99         n[ 0 .. n.length - 10 ]
 100       elsif n.downcase.end_with?( ".fasta" )
 101         n[ 0 .. n.length - 7 ]
 102       elsif n.downcase.end_with?( "_ni.fsa" )
 103         n[ 0 .. n.length - 8 ]
 104       elsif n.downcase.end_with?( ".fsa" )
 105         n[ 0 .. n.length - 5 ]
 106       else
 107         n
 108       end
 109     end
 110
 111     def error msg
 112       puts
 113       puts msg
 114       puts
 115       exit
 116     end
 117
 118   end
 119
 120   p = RunPhyloPipeline.new()
 121
 122   p.run()
 123
 124 end
 125
 126
 127