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 >= 2 && ARGV.length <= 4
  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       length      = ARGV[ 0 ].to_i
  31       e_value_exp = ARGV[ 1 ].to_i
  32
  33       e_for_hmmscan = 10
  34       hmmscan_option = "--nobias"
  35
  36       if ARGV.length == 4
  37         hmmscan_option = ARGV[ 3 ]
  38       end
  39       if ARGV.length == 3 || ARGV.length == 4
  40         e_for_hmmscan = ARGV[ 2 ].to_i
  41       end
  42
  43       if e_value_exp < 0
  44         error "E-value exponent for domain extraction cannot be negative"
  45       end
  46       if length <= 1
  47         error "length cannot be smaller than or equal to 1"
  48       end
  49       if e_for_hmmscan < 1
  50         error "E-value for hmmscan cannot be smaller than 1"
  51       end
  52
  53       input_files = Dir.entries(".").select { |f| !File.directory?( f ) && f.downcase.end_with?( ".fasta" ) }
  54
  55       puts "Input files:"
  56       input_files.each do | input |
  57         puts input
  58       end
  59       puts
  60
  61       counter = 1
  62       input_files.each do | input |
  63
  64         puts counter.to_s + "/" +  input_files.size.to_s + " " + input + ": "
  65
  66         counter += 1
  67
  68         hmm_name = ""
  69
  70         if input.downcase.end_with?( "_ni.fasta" )
  71           hmm_name = input[ 0 .. input.length - 10 ]
  72         elsif input.downcase.end_with?( ".fasta" )
  73           hmm_name = input[ 0 .. input.length - 7 ]
  74           puts
  75           puts "a. identifier normalization:"
  76           cmd = "#{TAP} #{input} #{hmm_name}_ni.fasta #{hmm_name}.nim"
  77           run_command( cmd )
  78           input = hmm_name + "_ni.fasta"
  79         else
  80           error "illegal name: " + input
  81         end
  82
  83         puts
  84         puts "b. hmmscan:"
  85         cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  86         run_command( cmd )
  87         puts
  88
  89         puts "c. hmmscan to simple domain table:"
  90         cmd = "#{HSP} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
  91         run_command( cmd )
  92         puts
  93
  94         puts "d. domain table to forester format:"
  95         cmd = "#{D2F} -e=10 #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
  96         run_command( cmd )
  97         puts
  98
  99         puts "e. dsx:"
 100         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}"
 101         run_command( cmd )
 102         puts
 103
 104       end
 105
 106     end
 107
 108     def run_command cmd
 109       puts cmd
 110       `#{cmd}`
 111     end
 112
 113     def get_base_name n
 114       if n.downcase.end_with?( "_ni.fasta" )
 115         n[ 0 .. n.length - 10 ]
 116       elsif n.downcase.end_with?( ".fasta" )
 117         n[ 0 .. n.length - 7 ]
 118       else
 119         error "illegal name: " + n
 120       end
 121     end
 122
 123     def error msg
 124       puts
 125       puts msg
 126       puts
 127       exit
 128     end
 129
 130   end
 131
 132   p = RunPhyloPipeline.new()
 133
 134   p.run()
 135
 136 end
 137
 138
 139