def main(debug=None):
args = docopt(__doc__, argv=debug, version=__version__)
if args["<vcf>"] == "":
print(__doc__)
v = vcf(args["<vcf>"])
for line in v.output_raw():
if line.startswith("#CHROM"):
line = line.split("\t")
if args["--subst"]:
find_replace = [re.split("[:=,]", x) for x in args["--subst"]]
for orig, replacement in find_replace:
for n, sample in enumerate(line[9:]):
if sample == orig:
line[9 + n] = replacement
if args["--prefix"]:
line[9:] = [args["--prefix"] + x for x in line[9:]]
if args["--suffix"]:
line[9:] = [x + args["--suffix"] for x in line[9:]]
print('\t'.join(line))
else:
print((line.strip()))
ANN_header = [
"allele", "effect", "impact", "gene_name", "gene_id", "feature_type",
"feature_id", "transcript_biotype", "exon_intron_rank", "nt_change",
"aa_change", "cDNA_position/cDNA_len", "protein_position",
"distance_to_feature", "error"
]
debug = None
if len(sys.argv) == 1:
debug = ['genome', "test.vcf.gz"]
if __name__ == '__main__':
args = docopt(__doc__, argv=debug, options_first=False)
module_path = os.path.split(os.path.realpath(__file__))[0]
v = vcf(args["<vcf>"])
field_set = []
if len(sys.argv) == 1:
print("Specify a VCF File")
sys.exit()
else:
info = [m.groupdict()["id"] for m in r_info.finditer(v.raw_header)]
format = [m.groupdict()["id"] for m in r_format.finditer(v.raw_header)]
# Construct Query String
print_header = ""
if args["--print-header"]:
print_header = "--print-header"
if args["long"]:
query_start = repr("%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t" +
'\t'.join(['%' + x
def main(debug=None):
args = docopt(__doc__,
version='VCF-Toolbox v0.1',
argv=debug,
options_first=False)
if args["--soft-filter"] and not args["--mode"]:
exit(message("Must Specify --mode with soft-filter"))
v = vcf(args["<vcf>"])
n_samples = len(v.samples) * 1.0
f = {}
filter_s = [
x for x in list(args.values())
if x in ["REF", "HET", "ALT", "MISSING"]
][0]
# Filter by rate or by number?
if args["--min"]:
direction = "<"
if int(float(args["--min"])) != float(args["--min"]):
filter_key_min = "r_" + filter_s
filter_val_min = float(args["--min"])
filter_type = "FREQUENCY"
else:
filter_key_min = filter_s
filter_val_min = int(float(args["--min"]))
filter_type = "COUNT"
filter_value = filter_val_min
if args["--max"]:
direction = ">"
if int(float(args["--max"])) != float(args["--max"]):
filter_key_max = "r_" + filter_s
filter_val_max = float(args["--max"])
filter_type = "FREQUENCY"
else:
filter_key_max = filter_s
filter_val_max = int(float(args["--max"]))
filter_type = "COUNT"
filter_value = filter_val_max
# Output header
header = v.raw_header.splitlines()
for n, i in enumerate(header):
if i.startswith("##FILTER") and args["--soft-filter"]:
filter_name = args["--soft-filter"]
filter_line = """##FILTER=<ID={filter_name},Description="Apply filter if {filter_type}({filter_s}) {direction} {filter_value}">""".format(
**locals())
header.insert(n + 1, filter_line)
break
header = '\n'.join(header) + "\n"
sys.stdout.write(header)
for line in v:
filtered = False
f["ALT"] = line.num_hom_alt
f["HET"] = line.num_het
f["REF"] = line.num_hom_ref
f["MISSING"] = int(n_samples - line.num_called)
f["r_ALT"] = f["ALT"] / n_samples
f["r_HET"] = f["HET"] / n_samples
f["r_REF"] = f["REF"] / n_samples
f["r_MISSING"] = f["MISSING"] / n_samples
if args["--min"]:
if f[filter_key_min] < filter_val_min:
filtered = True
if args["--max"]:
if f[filter_key_max] > filter_val_max:
filtered = True
if args["--soft-filter"]:
line = str(line).split("\t")
if args["--mode"] == "x":
line[6] = "PASS"
if filtered is False:
sys.stdout.write('\t'.join(line))
else:
if args["--mode"] == "+":
if line[6] == "PASS":
line[6] = ""
line[6] = ';'.join([line[6]] +
[args["--soft-filter"]]).strip(";")
elif args["--mode"] == "x":
line[6] = args["--soft-filter"]
sys.stdout.write('\t'.join(line))
elif filtered is False:
sys.stdout.write(str(line))