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/"
22 unless ARGV.length == 4
23 error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
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"
34 length = ARGV[ 2 ].to_i
35 e_value_exp = ARGV[ 3 ].to_i
36 do_domain_combination_analysis = true
39 error "e-value exponent cannot be negative"
42 error "length exponent cannot be smaller than or equal to 1"
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 ]
54 if do_domain_combination_analysis
57 cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{input}"
61 puts "hmmscan to simple domain table:"
62 cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
66 puts "domain table to forester format:"
67 cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{input} #{base_name}_hmmscan_10.dff"
74 cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{input}"
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}"
85 def run_command( cmd )
99 p = RunPhyloPipeline.new()