forester/ruby/evoruby/exe/run_phylo_pipeline_x.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     TAP       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/tap.rb"
  23
  24     def run
  25       unless ARGV.length >= 4 && ARGV.length <= 6
  26         error "arguments are:  <min-length> " +
  27          "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 10] [hmmscan option, default is --nobias, --max for no heuristics]"
  28       end
  29
  30
  31
  32       length      = ARGV[ 0 ].to_i
  33       e_value_exp = ARGV[ 1 ].to_i
  34
  35       e_for_hmmscan = 10
  36       hmmscan_option = "--nobias"
  37
  38       if ARGV.length == 4
  39         hmmscan_option = ARGV[ 3 ]
  40       end
  41       if ARGV.length == 3 || ARGV.length == 4
  42         e_for_hmmscan = ARGV[ 2 ].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       input_files = Dir.entries(".").select { |f| !File.directory?( f ) && f.downcase.end_with?( ".fasta" ) }
  56
  57       puts "Input files:"
  58       input_files.each do | input |
  59         puts input
  60       end
  61       puts
  62
  63       input_files.each do | input |
  64
  65         hmm_name = ""
  66
  67         if input.downcase.end_with?( "_ni.fasta" )
  68           hmm_name = input[ 0 .. input.length - 10 ]
  69         elsif input.downcase.end_with?( ".fasta" )
  70           hmm_name = input[ 0 .. input.length - 7 ]
  71           puts
  72           puts "0. identifier normalization:"
  73           cmd = "#{TAP} #{input}"
  74           run_command( cmd )
  75           puts
  76         else
  77           error "illegal name: " + input
  78         end
  79
  80         puts
  81         puts "1. hmmscan:"
  82         cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  83         run_command( cmd )
  84         puts
  85
  86         puts "2. hmmscan to simple domain table:"
  87         cmd = "#{HSP} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
  88         run_command( cmd )
  89         puts
  90
  91         puts "3. domain table to forester format:"
  92         cmd = "#{D2F} -e=10 #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
  93         run_command( cmd )
  94         puts
  95
  96         puts "4. dsx:"
  97         cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
  98         run_command( cmd )
  99         puts
 100
 101       end
 102
 103     end
 104
 105     def run_command cmd
 106       puts cmd
 107       `#{cmd}`
 108     end
 109
 110     def get_base_name n
 111       if n.downcase.end_with?( "_ni.fasta" )
 112         n[ 0 .. n.length - 10 ]
 113       elsif n.downcase.end_with?( ".fasta" )
 114         n[ 0 .. n.length - 7 ]
 115       else
 116         error "illegal name: " + n
 117       end
 118     end
 119
 120     def error msg
 121       puts
 122       puts msg
 123       puts
 124       exit
 125     end
 126
 127   end
 128
 129   p = RunPhyloPipeline.new()
 130
 131   p.run()
 132
 133 end
 134
 135
 136