def test_sync_splitmapper_execution():
gem.loglevel("debug")
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(input, index, results_dir + "/splitmap_out.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename == results_dir + "/splitmap_out.mapping"
assert os.path.exists(results_dir + "/splitmap_out.mapping")
assert sum(1 for x in mappings) == 10000
def test_sync_splitmapper_execution():
gem.loglevel("debug")
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(input, index,
results_dir + "/splitmap_out.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename == results_dir + "/splitmap_out.mapping"
assert os.path.exists(results_dir + "/splitmap_out.mapping")
assert sum(1 for x in mappings) == 10000
def gemtools():
try:
parser = argparse.ArgumentParser(prog="gemtools",
description="Gemtools driver to execute different gemtools command and pipelines"
)
parser.add_argument('--loglevel', dest="loglevel", default=None, help="Log level (error, warn, info, debug)")
parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + __VERSION__)
commands = {
"index": gem.production.Index,
"hash": gem.production.Hash,
"rna-pipeline": gem.production.RnaPipeline,
"t-index": gem.production.TranscriptIndex,
"merge": gem.production.Merge,
"gtf-junctions": gem.production.Junctions,
"denovo-junctions": gem.production.JunctionExtraction,
"stats": gem.production.Stats,
"report": gem.production.StatsReport
}
instances = {}
subparsers = parser.add_subparsers(title="commands", metavar="<command>", description="Available commands", dest="command")
for name, cmdClass in commands.items():
p = subparsers.add_parser(name, help=cmdClass.title, description=cmdClass.description)
instances[name] = cmdClass()
instances[name].register(p)
args = parser.parse_args()
if args.loglevel is not None:
gem.loglevel(args.loglevel)
# register cleanup signal handler
def cleanup_in_signal(signal, frame):
# cleanup
gem.utils.teminate_processes()
gem.files._cleanup()
signal.signal(signal.SIGINT, cleanup_in_signal)
signal.signal(signal.SIGQUIT, cleanup_in_signal)
signal.signal(signal.SIGHUP, cleanup_in_signal)
signal.signal(signal.SIGTERM, cleanup_in_signal)
try:
instances[args.command].run(args)
except gem.utils.CommandException, e:
sys.stderr.write("%s\n" % (str(e)))
exit(1)
except KeyboardInterrupt:
gem.utils.teminate_processes()
gem.files._cleanup()
exit(1)
finally:
# cleanup
gem.utils.teminate_processes()
gem.files._cleanup()
def gemtools():
try:
parser = argparse.ArgumentParser(
prog="gemtools",
description=
"Gemtools driver to execute different gemtools command and pipelines"
)
parser.add_argument('--loglevel',
dest="loglevel",
default=None,
help="Log level (error, warn, info, debug)")
parser.add_argument('-v',
'--version',
action='version',
version='%(prog)s ' + __VERSION__)
commands = {
"index": gem.production.Index,
"rna-pipeline": gem.production.RnaPipeline,
"t-index": gem.production.TranscriptIndex,
"gtfcount": gem.production.GtfCount,
"merge": gem.production.Merge,
"convert": gem.production.Convert,
"gtf-junctions": gem.production.Junctions,
"denovo-junctions": gem.production.JunctionExtraction,
"stats": gem.production.Stats,
"filter": gem.production.Filter,
"report": gem.production.StatsReport,
}
instances = {}
subparsers = parser.add_subparsers(title="commands",
metavar="<command>",
description="Available commands",
dest="command")
for name, cmdClass in commands.items():
p = subparsers.add_parser(name,
help=cmdClass.title,
description=cmdClass.description)
instances[name] = cmdClass()
instances[name].register(p)
args = parser.parse_args()
if args.loglevel is not None:
gem.loglevel(args.loglevel)
try:
instances[args.command].run(args)
except gem.utils.CommandException, e:
sys.stderr.write("%s\n" % (str(e)))
exit(1)
except KeyboardInterrupt:
exit(1)
finally:
pass
def gemtools():
try:
parser = argparse.ArgumentParser(prog="gemtools-cnv",
description="Gemtools-cnv driver to execute different gemtools-cnv command and pipelines"
)
parser.add_argument('--loglevel', dest="loglevel", default=None, help="Log level (error, warn, info, debug)")
parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + __VERSION__)
commands = {
"index": gem.production.Index,
"rna-pipeline": gem.production.RnaPipeline,
"basic-mapping": gem.production.BasicMappingPipeline,
"remove-duplicates": gem.production.RemoveDuplicatesPipeline,
"bam-2-fastq": gem.production.BamToFastqPipeline,
"fastq-splitter": gem.production.SplitFastqPipeline,
"cnv-mapping": gem.production.CnvMappingPipeline,
"cnv-call": gem.production.CnvCallingPipeline,
"cnv-assembly-preparation": gem.production.CnvAssemblyPreparation,
"cnv-prep": gem.production.CnvPrepare,
"t-index": gem.production.TranscriptIndex,
"gtfcount": gem.production.GtfCount,
"merge": gem.production.Merge,
"convert": gem.production.Convert,
"gtf-junctions": gem.production.Junctions,
"denovo-junctions": gem.production.JunctionExtraction,
"stats": gem.production.Stats,
"filter": gem.production.Filter,
"report": gem.production.StatsReport,
}
instances = {}
subparsers = parser.add_subparsers(title="commands", metavar="<command>", description="Available commands", dest="command")
for name, cmdClass in commands.items():
p = subparsers.add_parser(name, help=cmdClass.title, description=cmdClass.description)
instances[name] = cmdClass()
instances[name].register(p)
args = parser.parse_args()
if args.loglevel is not None:
gem.loglevel(args.loglevel)
try:
instances[args.command].run(args)
except gem.utils.CommandException, e:
sys.stderr.write("%s\n" % (str(e)))
exit(1)
except KeyboardInterrupt:
exit(1)
finally:
pass