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Update parser.py #156

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40 changes: 39 additions & 1 deletion maxatac/utilities/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,14 @@ def get_parser():
default=AUTOSOMAL_CHRS,
help="Chromosomes for averaging. Default: 1-22"
)

average_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to use."
)

average_parser.add_argument("-o", "--output", "--output_dir",
dest="output_dir",
Expand Down Expand Up @@ -223,6 +231,13 @@ def get_parser():
help="Genome sequence 2bit file."
)

predict_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to use.")

predict_parser.add_argument("-i", "-s", "--signal",
dest="signal",
type=str,
Expand Down Expand Up @@ -600,9 +615,17 @@ def get_parser():
type=str,
nargs="+",
default=AUTOSOMAL_CHRS,
help="Chromosomes for normalization. Default: 1-22"
help="Chromosomes for normalization. Default: 1-22 from the hg38 genome"
)

normalize_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to use."
)

normalize_parser.add_argument("-o", "--output", "--output_dir",
dest="output_dir",
type=str,
Expand Down Expand Up @@ -722,6 +745,13 @@ def get_parser():
max, mean, min"
)

benchmark_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to use.")

benchmark_parser.add_argument("--round_predictions",
dest="round_predictions",
type=int,
Expand Down Expand Up @@ -1015,6 +1045,14 @@ def get_parser():
help="The chromosomes to include in the final output."
)

prepare_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to use."
)

prepare_parser.add_argument("-t", "-threads", "--threads",
dest="threads",
type=int,
Expand Down