# Copyright:: Copyright (C) 2010 Christian M. Zmasek
# License:: GNU Lesser General Public License (LGPL)
#
-# $Id: run_phylo_pipeline.rb,v 1.15 2010/10/09 02:35:42 cmzmasek Exp $
+# $Id Exp $
#
#
-# hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm <BACTH_CHIPI>.fasta
-
-# hsp <BACTH_CHIPI>_hmmscan_240_10 <BACTH_CHIPI>_hmmscan_240_10_domain_table
-
-# d2f -e=10 <BACTH_CHIPI>_hmmscan_240_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_240_10.dff
-
-# hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD <~/DATA/PFAM/PFAM240/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
-
-# dsx -dd -e=<1e-2> -l=<200> <BACTH_CHIPI>.hmmsearch_SusD <BACTH_CHIPI>.fasta BACTH_CHIPI_e2_200
-
-
module Evoruby
class RunPhyloPipeline
+ PFAM = "/home/czmasek/DATA/PFAM/PFAM270X/"
+ HMMSCAN = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
+ HSP = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
+ D2F = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
+ DSX = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
+
def run
- unless ARGV.length == 4
- puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]"
- exit
+ unless ARGV.length >= 4 && ARGV.length <= 6
+ error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> " +
+ "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]"
end
- hmmscan = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmscan"
- hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmsearch"
- hsp = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/hsp.rb"
- d2f = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/d2f.rb"
- dsx = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/dsx.rb"
-
- base_name = ARGV[ 0 ]
+ input = ARGV[ 0 ]
hmm = ARGV[ 1 ]
- length = ARGV[ 2 ]
- e_value_exp = ARGV[ 3 ]
- do_domain_combination_analysis = true
+ length = ARGV[ 2 ].to_i
+ e_value_exp = ARGV[ 3 ].to_i
+
+ e_for_hmmscan = 20
+ hmmscan_option = "--nobias"
- if do_domain_combination_analysis
+ if ARGV.length == 6
+ hmmscan_option = ARGV[ 5 ]
+ end
+ if ARGV.length == 5 || ARGV.length == 6
+ e_for_hmmscan = ARGV[ 4 ].to_i
+ end
- cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm #{base_name}.fasta"
- run_command( cmd )
+ if e_value_exp < 0
+ error "E-value exponent for domain extraction cannot be negative"
+ end
+ if length <= 1
+ error "length cannot be smaller than or equal to 1"
+ end
+ if e_for_hmmscan < 1
+ error "E-value for hmmscan cannot be smaller than 1"
+ end
- cmd = "#{hsp} #{base_name}_hmmscan_240_10 #{base_name}_hmmscan_240_10_domain_table"
- run_command( cmd )
+ base_name = get_base_name input
- cmd = "#{d2f} -e=10 #{base_name}_hmmscan_240_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_240_10.dff"
- run_command( cmd )
+ puts
+ puts "1. hmmscan:"
+ cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
+ run_command( cmd )
+ puts
- end
+ puts "2. hmmscan to simple domain table:"
+ cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
+ run_command( cmd )
+ puts
- cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm} ~/DATA/PFAM/PFAM240/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
+ puts "3. domain table to forester format:"
+ cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
run_command( cmd )
+ puts
- cmd = "#{dsx} -dd -e=1e-#{e_value_exp.to_s} -l=#{length} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_e#{e_value_exp.to_s}_#{length}"
+ puts "4. dsx:"
+ 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}__ee#{e_value_exp.to_s}_#{length}"
run_command( cmd )
+ puts
end
- def run_command( cmd )
+ def run_command cmd
puts cmd
`#{cmd}`
end
+ def get_base_name n
+ if n.downcase.end_with?( "_ni.fasta" )
+ n[ 0 .. n.length - 10 ]
+ elsif n.downcase.end_with?( ".fasta" )
+ n[ 0 .. n.length - 7 ]
+ elsif n.downcase.end_with?( "_ni.fsa" )
+ n[ 0 .. n.length - 8 ]
+ elsif n.downcase.end_with?( ".fsa" )
+ n[ 0 .. n.length - 5 ]
+ else
+ n
+ end
+ end
+
+ def error msg
+ puts
+ puts msg
+ puts
+ exit
+ end
+
end
p = RunPhyloPipeline.new()
git://source.jalview.org / jalview.git / blobdiff