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
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
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