1 #!/usr/local/bin/ruby -w
5 # Copyright:: Copyright (C) 2010 Christian M. Zmasek
6 # License:: GNU Lesser General Public License (LGPL)
8 # $Id: run_phylo_pipeline.rb,v 1.15 2010/10/09 02:35:42 cmzmasek Exp $
13 # hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm <BACTH_CHIPI>.fasta
15 # hsp <BACTH_CHIPI>_hmmscan_250_10 <BACTH_CHIPI>_hmmscan_250_10_domain_table
17 # d2f -e=10 <BACTH_CHIPI>_hmmscan_250_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_250_10.dff
19 # hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD <~/DATA/PFAM/PFAM250/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
21 # dsx -dd -e=<1e-2> -l=<200> <BACTH_CHIPI>.hmmsearch_SusD <BACTH_CHIPI>.fasta BACTH_CHIPI_e2_200
26 class RunPhyloPipeline
29 unless ARGV.length == 4
30 puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]"
34 hmmscan = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
35 hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
36 hsp = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
37 d2f = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
38 dsx = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
43 e_value_exp = ARGV[ 3 ]
44 do_domain_combination_analysis = true
46 if do_domain_combination_analysis
48 cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm #{base_name}.fasta"
51 cmd = "#{hsp} #{base_name}_hmmscan_250_10 #{base_name}_hmmscan_250_10_domain_table"
54 cmd = "#{d2f} -e=10 #{base_name}_hmmscan_250_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_250_10.dff"
59 cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM250/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
62 cmd = "#{dsx} -dd -e=1e-#{e_value_exp.to_s} -l=#{length} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}"
67 def run_command( cmd )
74 p = RunPhyloPipeline.new()