diff --git a/maxatac/utilities/parser.py b/maxatac/utilities/parser.py index 840e748..43dccdb 100644 --- a/maxatac/utilities/parser.py +++ b/maxatac/utilities/parser.py @@ -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, @@ -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", @@ -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 @@ -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", @@ -580,20 +619,20 @@ 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", @@ -601,14 +640,30 @@ def get_parser(): 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", @@ -616,7 +671,7 @@ def get_parser(): type=int, default=0, help="The minimum value to use for normalization" - ) + ) normalize_parser.add_argument("--max", dest="max", @@ -624,7 +679,7 @@ def get_parser(): required=False, default=False, help="The maximum value to use for normalization" - ) + ) normalize_parser.add_argument("--clip", dest="clip", @@ -632,21 +687,21 @@ def get_parser(): 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", @@ -654,13 +709,13 @@ def get_parser(): 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 @@ -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, @@ -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", @@ -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, @@ -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",