module EcfClassify::HMMER
Constants
- DBLOCATION
Public Class Methods
hmmpress(file)
click to toggle source
# File lib/ecf_classify/hmmer.rb, line 35 def self.hmmpress(file) Dir.glob("#{file}.h3{i,f,m,p}").each { |f| File.delete(f) } cmd = "hmmpress #{file}" out = `#{cmd}` return [out, $?.exitstatus ] end
hmmscan(infile, outfile, db)
click to toggle source
# File lib/ecf_classify/hmmer.rb, line 10 def self.hmmscan(infile, outfile, db) if DBLOCATION.key? db hmm = Utils.path(DBLOCATION[db]) cmd = "hmmscan --noali --domtblout #{outfile} #{Utils.path(DBLOCATION[db])} #{infile} 2>&1" out = `#{cmd}` return [out,$?.exitstatus] else return ["No such database", 2] end end
hmmsearch(infile, outfile, db)
click to toggle source
# File lib/ecf_classify/hmmer.rb, line 21 def self.hmmsearch(infile, outfile, db) unless EcfClassify::Zenodo.status EcfClassify::Zenodo.download end if EcfClassify::Zenodo::FILES.key? db hmm = EcfClassify::Zenodo.path(db) cmd = "hmmsearch --noali --domtblout #{outfile} #{hmm} #{infile} 2>&1" out = `#{cmd}` return [out, $?.exitstatus] else return ["No such database", 2] end end