1 #!/usr/local/bin/ruby -w
5 # Copyright:: Copyright (C) 2010 Christian M. Zmasek
6 # License:: GNU Lesser General Public License (LGPL)
15 class RunPhyloPipeline
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"
25 unless ARGV.length == 4
26 error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
34 length = ARGV[ 2 ].to_i
35 e_value_exp = ARGV[ 3 ].to_i
37 hmmscan_option = "--nobias"
41 error "e-value exponent cannot be negative"
44 error "length exponent cannot be smaller than or equal to 1"
48 if input.downcase.end_with?( ".fasta" )
49 base_name = input[ 0 .. input.length - 7 ]
50 elsif input.downcase.end_with?( ".fsa" )
51 base_name = input[ 0 .. input.length - 5 ]
57 cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
61 puts "2. hmmscan to simple domain table:"
62 cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
66 puts "3. domain table to forester format:"
67 cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
72 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}_e#{e_value_exp.to_s}_#{length}"
78 def run_command( cmd )
92 p = RunPhyloPipeline.new()