Commit ed5b112d authored by MARIJON Pierre's avatar MARIJON Pierre

snakemake can manage mutual exclusion and use '--' to separate knot and snakemake parameter

parent 3cea3672
......@@ -22,17 +22,17 @@ def main(args = None):
parser = argparse.ArgumentParser(prog="KNOT")
# # avaible
# # b e g i m o q u w x y z
# # A B C E G H I J K L M N Q V W X Y Z
parser.add_argument("-C", "--contigs", required=True,
parser.add_argument("-c", "--contigs", required=True,
help="fasta file than contains contigs")
parser.add_argument("-g", "--contigs_graph",
help="contigs graph")
parser.add_argument("-i", "--raw-reads",
help="read used for assembly")
parser.add_argument("-m", "--correct-reads",
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument("-r", "--raw-reads",
help="read used for assembly")
group.add_argument("-C", "--correct-reads",
help="read used for assembly")
parser.add_argument("-o", "--output", required=True,
help="output prefix")
parser.add_argument("--contig-min-length", default=100000, type=int,
......@@ -40,10 +40,10 @@ def main(args = None):
parser.add_argument("--read-type", choices=["pb", "ont"], default="pb",
help="type of input read, default pb")
parser.add_argument("--help-all", action='store_true',
help="Show knot help and snakemake help")
help="show knot help and snakemake help")
args, unknow_arg = parser.parse_known_args(args)
args = vars(args)
# Check parameter
## raw_reads or correct
if args["help_all"]:
......@@ -51,19 +51,6 @@ def main(args = None):
return 1
go_out = False
if args["raw_reads"] is None and args["correct_reads"] is None:
print("You need set --raw-reads or --correct-reads\n", file=sys.stderr)
go_out = True
if args["raw_reads"] is not None and args["correct_reads"] is not None:
print("You can't set --raw-reads and --correct-reads at same time\n", file=sys.stderr)
go_out = True
if go_out:
return 1
## if contig graph isn't set generate empty file
if args["contigs_graph"] is None:
args["contigs_graph"] = tempfile.NamedTemporaryFile(delete=False).name
......@@ -93,7 +80,7 @@ def main(args = None):
"--snakefile", snakemake_rule
call += unknow_arg
call += unknow_arg[1:]
print(" ".join(call))
out =
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