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 require 'fileutils'
  13
  14 module Evoruby
  15
  16   class RunPhyloPipeline
  17
  18     LAUNCH_ANALYSIS = true
  19     HOME          = "/home/czmasek/"
  20     FORESTER_RUBY = "#{HOME}SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/"
  21     PFAM          = "#{HOME}DATA/PFAM/PFAM270X/"
  22     HMMSCAN       = "#{HOME}SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
  23     HSP           = "#{FORESTER_RUBY}hsp.rb"
  24     D2F           = "#{FORESTER_RUBY}d2f.rb"
  25     DSX           = "#{FORESTER_RUBY}dsx.rb"
  26     TAP           = "#{FORESTER_RUBY}tap.rb"
  27     PF            = "#{FORESTER_RUBY}phylogeny_factory.rb"
  28     TEMPLATE_FILE = '00_phylogeny_factory.template'
  29
  30     def run
  31       unless ARGV.length >= 2 && ARGV.length <= 4
  32         error "arguments are:  <min-length> " +
  33          "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 10] [hmmscan option, default is --nobias, --max for no heuristics]"
  34       end
  35
  36       length      = ARGV[ 0 ].to_i
  37       e_value_exp = ARGV[ 1 ].to_i
  38
  39       e_for_hmmscan = 10
  40       hmmscan_option = "--nobias"
  41
  42       if ARGV.length == 4
  43         hmmscan_option = ARGV[ 3 ]
  44       end
  45       if ARGV.length == 3 || ARGV.length == 4
  46         e_for_hmmscan = ARGV[ 2 ].to_i
  47       end
  48
  49       if e_value_exp < 0
  50         error "E-value exponent for domain extraction cannot be negative"
  51       end
  52       if length <= 1
  53         error "length cannot be smaller than or equal to 1"
  54       end
  55       if e_for_hmmscan < 1
  56         error "E-value for hmmscan cannot be smaller than 1"
  57       end
  58
  59       input_files = Dir.entries(".").select { |f| !File.directory?( f ) && f.downcase.end_with?( ".fasta" ) }
  60
  61       puts "Input files:"
  62       input_files.each do | input |
  63         puts input
  64       end
  65       puts
  66
  67       counter = 1
  68       input_files.each do | input |
  69
  70         puts counter.to_s + "/" +  input_files.size.to_s + " " + input + ": "
  71
  72         counter += 1
  73
  74         hmm_name = ""
  75         id_norm = false
  76         orig_input = input
  77
  78         if input.downcase.end_with?( "_ni.fasta" )
  79           hmm_name = input[ 0 .. input.length - 10 ]
  80         elsif input.downcase.end_with?( ".fasta" )
  81           id_norm = true
  82           hmm_name = input[ 0 .. input.length - 7 ]
  83           puts
  84           puts "a. identifier normalization:"
  85           cmd = "#{TAP} #{input} #{hmm_name}_ni.fasta #{hmm_name}.nim"
  86           run_command( cmd )
  87           input = hmm_name + "_ni.fasta"
  88         else
  89           error "illegal name: " + input
  90         end
  91
  92         Dir.mkdir( hmm_name )
  93
  94         puts
  95         puts "b. hmmscan:"
  96         cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
  97         run_command( cmd )
  98         puts
  99
 100         puts "c. hmmscan to simple domain table:"
 101         cmd = "#{HSP} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
 102         run_command( cmd )
 103         puts
 104
 105         puts "d. domain table to forester format:"
 106         cmd = "#{D2F} -e=10 #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
 107         run_command( cmd )
 108         puts
 109
 110         puts "e. dsx:"
 111         cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmm_name}/#{hmm_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
 112         run_command( cmd )
 113         puts
 114
 115         if id_norm
 116           FileUtils.mv "#{hmm_name}_ni.fasta", "#{hmm_name}/#{hmm_name}_ni.fasta"
 117           FileUtils.mv "#{hmm_name}.nim", "#{hmm_name}/#{hmm_name}.nim"
 118           FileUtils.cp orig_input, "#{hmm_name}/#{orig_input}"
 119         end
 120
 121         Dir.mkdir( hmm_name + "/msa" )
 122         Dir.mkdir( hmm_name + "/msa100" )
 123
 124         FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
 125         FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa100/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
 126
 127         if File.exists?( TEMPLATE_FILE )
 128           FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa/"
 129           FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa100/"
 130
 131           if LAUNCH_ANALYSIS
 132             puts "f. analysis:"
 133             Dir.chdir "#{hmm_name}/msa/"
 134             run_command "#{PF} -b=1 -s"
 135             Dir.chdir "../.."
 136             Dir.chdir "#{hmm_name}/msa100/"
 137             run_command "#{PF} -b=100 -s"
 138             Dir.chdir "../.."
 139             puts
 140           end
 141         end
 142
 143       end
 144
 145     end
 146
 147     def run_command cmd
 148       puts cmd
 149       `#{cmd}`
 150     end
 151
 152     def get_base_name n
 153       if n.downcase.end_with?( "_ni.fasta" )
 154         n[ 0 .. n.length - 10 ]
 155       elsif n.downcase.end_with?( ".fasta" )
 156         n[ 0 .. n.length - 7 ]
 157       else
 158         error "illegal name: " + n
 159       end
 160     end
 161
 162     def error msg
 163       puts
 164       puts msg
 165       puts
 166       exit
 167     end
 168
 169   end
 170
 171   p = RunPhyloPipeline.new()
 172
 173   p.run()
 174
 175 end
 176
 177
 178