Esempio n. 1
0
def FindScaffoldORFS(input,output):
   if "FindScaffoldORFS" in _skipsteps:
      run_process(_settings, "touch %s/FindScaffoldORFS/out/%s.scaffolds.faa"%(_settings.rundir, _settings.PREFIX))
      return 0
   if _orf == "metagenemark":
       if not os.path.exists(_settings.METAGENEMARK + os.sep + "gmhmmp"):
          print "Error: MetaGeneMark not found in %s. Please check your path and try again.\n"%(_settings.METAGENEMARK)
          raise(JobSignalledBreak)
       run_process(_settings, "%s/gmhmmp -o %s/FindScaffoldORFS/out/%s.scaffolds.orfs -m %s/config/MetaGeneMark_v1.mod -d -a %s/Scaffold/out/%s.linearize.scaffolds.final"%(_settings.METAGENEMARK,_settings.rundir,_settings.PREFIX,_settings.METAMOS_UTILS,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
       parse_genemarkout("%s/FindScaffoldORFS/out/%s.scaffolds.orfs"%(_settings.rundir,_settings.PREFIX),1, "FindScaffoldORFS")
   elif _orf == "fraggenescan":
       if not os.path.exists(_settings.FRAGGENESCAN + os.sep + "FragGeneScan"):
          print "Error: FragGeneScan not found in %s. Please check your path and try again.\n"%(_settings.FRAGGENESCAN)
          raise(JobSignalledBreak)
       run_process(_settings,"%s/FragGeneScan -s %s/Scaffold/out/%s.linearize.scaffolds.final -o %s/FindScaffoldORFS/out/%s.orfs -w 0 -t complete"%(_settings.FRAGGENESCAN,_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX))
       parse_fraggenescanout("%s/FindScaffoldORFS/out/%s.orfs"%(_settings.rundir,_settings.PREFIX), 1, "FindScaffoldORFS")
       run_process(_settings,"cp %s/FindScaffoldORFS/out/%s.orfs.ffn %s/FindScaffoldORFS/out/%s.fna"%(_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
       run_process(_settings,"cp %s/FindScaffoldORFS/out/%s.orfs.faa %s/FindScaffoldORFS/out/%s.faa"%(_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
   else:
       #not recognized
       return 1
Esempio n. 2
0
def FindScaffoldORFS(input,output):
   if "FindScaffoldORFS" in _skipsteps:
      run_process(_settings, "touch %s/FindScaffoldORFS/out/%s.scaffolds.faa"%(_settings.rundir, _settings.PREFIX))
      run_process(_settings, "touch %s/Logs/findscaffoldorfs.skip"%(_settings.rundir), "FindScaffoldORFS")
      return 0
   if _orf == "metagenemark":
       if not os.path.exists(_settings.METAGENEMARK + os.sep + "gmhmmp"):
          print "Error: MetaGeneMark not found in %s. Please check your path and try again.\n"%(_settings.METAGENEMARK)
          raise(JobSignalledBreak)
       run_process(_settings, "%s/gmhmmp -o %s/FindScaffoldORFS/out/%s.scaffolds.orfs -m %s/config/MetaGeneMark_v1.mod -d -a %s/Scaffold/out/%s.linearize.scaffolds.final"%(_settings.METAGENEMARK,_settings.rundir,_settings.PREFIX,_settings.METAMOS_UTILS,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
       parse_genemarkout("%s/FindScaffoldORFS/out/%s.scaffolds.orfs"%(_settings.rundir,_settings.PREFIX),1, "FindScaffoldORFS")
   elif _orf == "fraggenescan":
       if not os.path.exists(_settings.FRAGGENESCAN + os.sep + "FragGeneScan"):
          print "Error: FragGeneScan not found in %s. Please check your path and try again.\n"%(_settings.FRAGGENESCAN)
          raise(JobSignalledBreak)
       run_process(_settings,"%s/FragGeneScan -s %s/Scaffold/out/%s.linearize.scaffolds.final -o %s/FindScaffoldORFS/out/%s.orfs -w 0 -t complete"%(_settings.FRAGGENESCAN,_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
       parse_fraggenescanout("%s/FindScaffoldORFS/out/%s.orfs"%(_settings.rundir,_settings.PREFIX), 1, "FindScaffoldORFS")
       run_process(_settings,"cp %s/FindScaffoldORFS/out/%s.orfs.ffn %s/FindScaffoldORFS/out/%s.fna"%(_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
       run_process(_settings,"cp %s/FindScaffoldORFS/out/%s.orfs.faa %s/FindScaffoldORFS/out/%s.faa"%(_settings.rundir,_settings.PREFIX,_settings.rundir,_settings.PREFIX),"FindScaffoldORFS")
   elif _orf == "prokka":
      if not os.path.exists(_settings.PROKKA + os.sep + "prokka"):
         print "Error: Prokka not found in %s. Please check your paths and try again"%(_settings.PROKKA)
         raise(JobSignalledBreak)

      prokkaOptions = getProgramParams(_settings.METAMOS_UTILS, "prokka.spec", "", "-")
      if "--gram" in prokkaOptions and not os.path.exists(_settings.SIGNALP + os.sep + "signalp"):
         print "Warning: Prokka option --gram requires SignalP which is not found. Disabling"
         prokkaOptions = prokkaOptions.replace("--gram", "")

      run_process(_settings, "%s/prokka --outdir %s/FindScaffoldORFS/out/prokka --prefix %s --force %s/Scaffold/out/%s.linearize.scaffolds.final"%(_settings.PROKKA, _settings.rundir, _settings.PREFIX, _settings.rundir, _settings.PREFIX), "FindScaffoldORFS")
      parse_prokka("%s/FindScaffoldORFS/out/prokka/%s.gff"%(_settings.rundir,_settings.PREFIX), 1, "FindScaffoldORFS")

      run_process(_settings, "ln %s/FindScaffoldORFS/out/prokka/%s.ffn %s/FindScaffoldORFS/out/%s.fna"%(_settings.rundir, _settings.PREFIX, _settings.rundir, _settings.PREFIX), "FindScaffoldORFS")
      run_process(_settings, "ln %s/FindScaffoldORFS/out/prokka/%s.faa %s/FindScaffoldORFS/out/%s.faa"%(_settings.rundir, _settings.PREFIX, _settings.rundir, _settings.PREFIX), "FindScaffoldORFS")
   else:
       #not recognized
       return 1
Esempio n. 3
0
def FindScaffoldORFS(input, output):
    if "FindScaffoldORFS" in _skipsteps:
        run_process(
            _settings, "touch %s/FindScaffoldORFS/out/%s.scaffolds.faa" %
            (_settings.rundir, _settings.PREFIX))
        run_process(_settings,
                    "touch %s/Logs/findscaffoldorfs.skip" % (_settings.rundir),
                    "FindScaffoldORFS")
        return 0
    if _orf == "metagenemark":
        if not os.path.exists(_settings.METAGENEMARK + os.sep + "gmhmmp"):
            print "Error: MetaGeneMark not found in %s. Please check your path and try again.\n" % (
                _settings.METAGENEMARK)
            raise (JobSignalledBreak)
        run_process(
            _settings,
            "%s/gmhmmp -o %s/FindScaffoldORFS/out/%s.scaffolds.orfs -m %s/config/MetaGeneMark_v1.mod -d -a %s/Scaffold/out/%s.linearize.scaffolds.final"
            % (_settings.METAGENEMARK, _settings.rundir, _settings.PREFIX,
               _settings.METAMOS_UTILS, _settings.rundir, _settings.PREFIX),
            "FindScaffoldORFS")
        parse_genemarkout(
            "%s/FindScaffoldORFS/out/%s.scaffolds.orfs" %
            (_settings.rundir, _settings.PREFIX), 1, "FindScaffoldORFS")
    elif _orf == "fraggenescan":
        if not os.path.exists(_settings.FRAGGENESCAN + os.sep +
                              "FragGeneScan"):
            print "Error: FragGeneScan not found in %s. Please check your path and try again.\n" % (
                _settings.FRAGGENESCAN)
            raise (JobSignalledBreak)
        run_process(
            _settings,
            "%s/FragGeneScan -s %s/Scaffold/out/%s.linearize.scaffolds.final -o %s/FindScaffoldORFS/out/%s.orfs -w 0 -t complete"
            % (_settings.FRAGGENESCAN, _settings.rundir, _settings.PREFIX,
               _settings.rundir, _settings.PREFIX), "FindScaffoldORFS")
        parse_fraggenescanout(
            "%s/FindScaffoldORFS/out/%s.orfs" %
            (_settings.rundir, _settings.PREFIX), 1, "FindScaffoldORFS")
        run_process(
            _settings,
            "cp %s/FindScaffoldORFS/out/%s.orfs.ffn %s/FindScaffoldORFS/out/%s.fna"
            % (_settings.rundir, _settings.PREFIX, _settings.rundir,
               _settings.PREFIX), "FindScaffoldORFS")
        run_process(
            _settings,
            "cp %s/FindScaffoldORFS/out/%s.orfs.faa %s/FindScaffoldORFS/out/%s.faa"
            % (_settings.rundir, _settings.PREFIX, _settings.rundir,
               _settings.PREFIX), "FindScaffoldORFS")
    elif _orf == "prokka":
        if not os.path.exists(_settings.PROKKA + os.sep + "prokka"):
            print "Error: Prokka not found in %s. Please check your paths and try again" % (
                _settings.PROKKA)
            raise (JobSignalledBreak)

        libUpdate = "%s/lib/" % (os.path.dirname(_settings.PROKKA))
        if "PERL5LIB" in os.environ:
            libUpdate = "%s%s%s" % (os.environ["PERL5LIB"], os.pathsep,
                                    libUpdate)
        os.environ["PERL5LIB"] = libUpdate
        print "The path for proka is %s" % (libUpdate)
        prokkaOptions = getProgramParams(_settings.METAMOS_UTILS,
                                         "prokka.spec", "", "-")
        if "--gram" in prokkaOptions and not os.path.exists(_settings.SIGNALP +
                                                            os.sep +
                                                            "signalp"):
            print "Warning: Prokka option --gram requires SignalP which is not found. Disabling"
            prokkaOptions = prokkaOptions.replace("--gram", "")

        run_process(
            _settings,
            "%s/prokka --outdir %s/FindScaffoldORFS/out/prokka --prefix %s --force %s/Scaffold/out/%s.linearize.scaffolds.final"
            % (_settings.PROKKA, _settings.rundir, _settings.PREFIX,
               _settings.rundir, _settings.PREFIX), "FindScaffoldORFS")
        parse_prokka(
            "%s/FindScaffoldORFS/out/prokka/%s.gff" %
            (_settings.rundir, _settings.PREFIX), 1, "FindScaffoldORFS")

        run_process(
            _settings,
            "ln %s/FindScaffoldORFS/out/prokka/%s.ffn %s/FindScaffoldORFS/out/%s.fna"
            % (_settings.rundir, _settings.PREFIX, _settings.rundir,
               _settings.PREFIX), "FindScaffoldORFS")
        run_process(
            _settings,
            "ln %s/FindScaffoldORFS/out/prokka/%s.faa %s/FindScaffoldORFS/out/%s.faa"
            % (_settings.rundir, _settings.PREFIX, _settings.rundir,
               _settings.PREFIX), "FindScaffoldORFS")
    else:
        #not recognized
        return 1