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Update parser.py #167

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113 changes: 99 additions & 14 deletions maxatac/utilities/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,6 +176,22 @@ def get_parser():
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 which the input file was aligned."
)

average_parser.add_argument("--max_zooms",
dest="max_zooms",
type=int,
default=5,
required=False,
help="The number of zoom levels that should be computed for the averaged bigWig file."
)

average_parser.add_argument("-o", "--output", "--output_dir",
dest="output_dir",
type=str,
Expand Down Expand Up @@ -222,6 +238,22 @@ def get_parser():
type=str,
help="Genome sequence 2bit file."
)

predict_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to which the input file was aligned."
)

average_parser.add_argument("--max_zooms",
dest="max_zooms",
type=int,
default=5,
required=False,
help="The number of zoom levels that should be computed for the output bigWig file."
)

predict_parser.add_argument("-i", "-s", "--signal",
dest="signal",
Expand Down Expand Up @@ -329,6 +361,13 @@ def get_parser():
required=False,
help="Skip calling peaks on prediction tracks"
)

predict_parser.add_argument("--threads",
dest="threads",
type=int,
default=24,
help="Number of processes to run prediction in parallel. Default: 24."
)

#############################################
# Train parser
Expand All @@ -347,7 +386,7 @@ def get_parser():
type=str,
default="hg38",
required=False,
help="The reference genome build to use."
help="The reference genome build to which the input file was aligned."
)

train_parser.add_argument("--sequence",
Expand Down Expand Up @@ -580,87 +619,103 @@ def get_parser():
type=str,
required=True,
help="Input .bigwig file."
)
)

normalize_parser.add_argument("-n", "--name", "--prefix",
required=True,
dest="name",
type=str,
help="Name to use for filename"
)
)

normalize_parser.add_argument("-cs", "--chrom_sizes", "--chromosome_sizes",
dest="chrom_sizes",
type=str,
help="Chrom sizes file"
)
)

normalize_parser.add_argument("-c", "--chroms", "--chromosomes",
dest="chromosomes",
type=str,
nargs="+",
default=AUTOSOMAL_CHRS,
help="Chromosomes for normalization. Default: 1-22"
)
)

normalize_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to which the input file was aligned."
)

normalize_parser.add_argument("--max_zooms",
dest="max_zooms",
type=int,
default=5,
required=False,
help="The number of zoom levels that should be computed for the normalized bigWig file."
)

normalize_parser.add_argument("-o", "--output", "--output_dir",
dest="output_dir",
type=str,
default=os.getcwd(),
help="Output directory. Default: Output to current working directory."
)
)

normalize_parser.add_argument("--min",
dest="min",
required=False,
type=int,
default=0,
help="The minimum value to use for normalization"
)
)

normalize_parser.add_argument("--max",
dest="max",
type=int,
required=False,
default=False,
help="The maximum value to use for normalization"
)
)

normalize_parser.add_argument("--clip",
dest="clip",
type=bool,
required=False,
default=False,
help="Whether to clip minmax values to the range 0,1"
)
)

normalize_parser.add_argument("--method",
dest="method",
type=str,
default="min-max",
help="The method to use for normalization"
)
)

normalize_parser.add_argument("--max_percentile",
dest="max_percentile",
type=int,
default=99,
help="The maximum percentile to use for normalization"
)
)

normalize_parser.add_argument("--loglevel",
dest="loglevel",
type=str,
default="info",
choices=LOG_LEVELS.keys(),
help="Logging level. Default: " + DEFAULT_LOG_LEVEL
)
)

normalize_parser.add_argument("--blacklist_bw",
dest="blacklist_bw",
type=str,
help="The blacklisted regions to exclude (BigWig file format)"
)
)

#############################################
# Benchmark subparser
Expand Down Expand Up @@ -722,6 +777,14 @@ 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 which the input file was aligned."
)

benchmark_parser.add_argument("--round_predictions",
dest="round_predictions",
type=int,
Expand Down Expand Up @@ -887,7 +950,7 @@ def get_parser():
type=str,
default="hg38",
required=False,
help="The reference genome build to use."
help="The reference genome build to which the input file was aligned."
)

variants_parser.add_argument("-s", "--sequence",
Expand Down Expand Up @@ -1015,6 +1078,14 @@ 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 which the input file was aligned."
)

prepare_parser.add_argument("-t", "-threads", "--threads",
dest="threads",
type=int,
Expand Down Expand Up @@ -1091,12 +1162,26 @@ def get_parser():
choices=LOG_LEVELS.keys(),
help="Logging level. Default: " + DEFAULT_LOG_LEVEL
)

threshold_parser.add_argument("--genome",
dest="genome",
type=str,
default="hg38",
required=False,
help="The reference genome build to which the input BAM file was aligned."
)

threshold_parser.add_argument("--blacklist_bw",
dest="blacklist_bw",
type=str,
help="The blacklisted regions to exclude in bigwig format."
)

threshold_parser.add_argument("--blacklist_bed",
dest="blacklist_bed",
type=str,
help="The blacklisted regions to exclude in bigwig format."
)

threshold_parser.add_argument("--meta_file",
dest="meta_file",
Expand Down