class RunPhyloPipeline
- PFAM = "/home/czmasek/DATA/PFAM/PFAM260X/"
+ 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 && 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]"
+ "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]"
end
input = ARGV[ 0 ]
base_name = get_base_name input
+ 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
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}"
+ 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