def run(self, args):
## parsing command line arguments
try:
## initialize pipeline and check values
pipeline = MappingPipeline(args=args)
except PipelineError, e:
sys.stderr.write("\nERROR: " + e.message + "\n")
exit(1)
def register(self, parser):
pipeline = MappingPipeline()
general_group = parser.add_argument_group('General')
## general pipeline paramters
general_group.add_argument('-f', '--files', dest="input", nargs="+", metavar="input",
help='''Single fastq input file or both files for a paired-end run separated by space.
Note that if you specify only one file, we will look for the file containing the other pairs
automatically and start a paired-end run. Add the --single-end parameter to disable
pairing and file search. The file search for the second pair detects pairs
ending in [_|.|-][0|1|2].[fq|fastq|txt][.gz].''')
general_group.add_argument('--single-end', dest="single_end", action="store_true", default=None, help="Single end reads")
general_group.add_argument('-q', '--quality', dest="quality", metavar="quality",
default=pipeline.quality, help='Quality offset. 33, 64 or "ignore" to disable qualities.')
general_group.add_argument('-i', '--index', dest="index", metavar="index", help='Path to the .gem genome index')
general_group.add_argument('-a', '--annotation', dest="gtf", metavar="gtf", help='Path to the .gtf annotation that will be used to keep junctions even if the site does not have enough coverage.')
general_group.add_argument('--dry', dest="dry", action="store_true", default=None, help="Print and write configuration but do not start the pipeline")
general_group.add_argument('-t', '--threads', dest="threads", metavar="threads", type=int, help="Number of threads to use. Default %d" % pipeline.threads)
pipeline.register_junctions(parser)
def register(self, parser):
pipeline = MappingPipeline()
general_group = parser.add_argument_group('General')
## general pipeline paramters
general_group.add_argument('-f', '--files', dest="input", nargs="+", metavar="input",
help='''Single fastq input file or both files for a paired-end run separated by space.
Note that if you specify only one file, we will look for the file containing the other pairs
automatically and start a paired-end run. Add the --single-end parameter to disable
pairing and file search. The file search for the second pair detects pairs
ending in [_|.|-][0|1|2].[fq|fastq|txt][.gz].''')
general_group.add_argument('--single-end', dest="single_end", action="store_true", default=None, help="Single end reads")
general_group.add_argument('-q', '--quality', dest="quality", metavar="quality",
default=pipeline.quality, help='Quality offset. 33, 64 or "ignore" to disable qualities.')
general_group.add_argument('-i', '--index', dest="index", metavar="index", help='Path to the .gem genome index')
general_group.add_argument('-a', '--annotation', dest="gtf", metavar="gtf", help='Path to the .gtf annotation that will be used to keep junctions even if the site does not have enough coverage.')
general_group.add_argument('--dry', dest="dry", action="store_true", default=None, help="Print and write configuration but do not start the pipeline")
general_group.add_argument('-t', '--threads', dest="threads", metavar="threads", type=int, help="Number of threads to use. Default %d" % pipeline.threads)
pipeline.register_junctions(parser)
def register(self, parser):
pipeline = MappingPipeline()
pipeline.register_parameter(parser)
def register(self, parser):
pipeline = MappingPipeline()
pipeline.register_parameter(parser)
