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
  19
  20
  21     def run
  22       unless ARGV.length == 4
  23         error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
  24       end
  25
  26       hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
  27       hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
  28       hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
  29       d2f       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
  30       dsx       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
  31
  32       input       = ARGV[ 0 ]
  33       hmm         = ARGV[ 1 ]
  34       length      = ARGV[ 2 ]
  35       e_value_exp = ARGV[ 3 ]
  36       do_domain_combination_analysis = true
  37
  38       if e_value_exp < 0
  39         error "e-value exponent cannot be negative"
  40       end
  41       if length <= 1
  42         error "length exponent cannot be smaller than or equal to 1"
  43       end
  44
  45       base_name = nil
  46       if input.downcase.end_with?( ".fasta" )
  47         base_name = input[ 0 .. input.length - 7 ]
  48       elsif input.downcase.end_with?( ".fsa" )
  49         base_name = input[ 0 .. input.length - 5 ]
  50       else
  51          base_name = input
  52       end
  53
  54       if do_domain_combination_analysis
  55
  56         puts "hmmscan:"
  57         cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{input}"
  58         run_command( cmd )
  59         puts
  60
  61         puts "hmmscan to simple domain table:"
  62         cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
  63         run_command( cmd )
  64         puts
  65
  66         puts "domain table to forester format:"
  67         cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{input} #{base_name}_hmmscan_10.dff"
  68         run_command( cmd )
  69         puts
  70
  71       end
  72
  73       puts "hmmsearch:"
  74       cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{input}"
  75       run_command( cmd )
  76       puts
  77
  78       puts "dsx:"
  79       cmd = "#{dsx} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}.hmmsearch_#{hmm} #{input} #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}"
  80       run_command( cmd )
  81       puts
  82
  83     end
  84
  85     def run_command( cmd )
  86       puts cmd
  87       `#{cmd}`
  88     end
  89
  90     def error msg
  91       puts
  92       puts msg
  93       puts
  94       exit
  95     end
  96
  97   end
  98
  99   p = RunPhyloPipeline.new()
 100
 101   p.run()
 102
 103 end
 104
 105
 106