from conifertools import CallTable
import argparse
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--infile", "-i", action="store", required=True)
parser.add_argument("--outfile", "-o", action="store", required=True)
parser.add_argument("--gamma",
type=float,
action="store",
required=False,
default=0.9)
parser.add_argument("--cophenetic_cutoff",
type=float,
action="store",
required=False,
default=0.85)
args = parser.parse_args()
assert args.gamma <= 1, "Gamma must be <= 1.00"
assert args.cophenetic_cutoff <= 1, "All cophenetic cutoffs must be <= 1.00"
calls = CallTable(args.infile)
calls = calls.clusterCalls(gamma=args.gamma,
cophenetic_cutoff=args.cophenetic_cutoff)
calls.save(args.outfile)
import argparse
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--infile", "-i", action="store", required=True)
parser.add_argument("--cohort", action="store", required=True)
parser.add_argument("--esp_infile", action="store", required=True)
parser.add_argument("--outfile", "-o", action="store", required=True)
parser.add_argument("--gamma", type=float, action="store", required=False, default=0.9)
parser.add_argument("--cophenetic_cutoff", type=float, action="store", required=False, default=0.85)
args = parser.parse_args()
assert args.gamma <= 1, "Gamma must be <= 1.00"
assert args.cophenetic_cutoff <= 1, "Cophenetic cutoffs must be <= 1.00"
calls = CallTable(args.infile)
esp_calls = CallTable(args.esp_infile)
calls.calls["cohort"] = args.cohort
esp_calls.calls["cohort"] = "ESP"
calls.appendCalls(esp_calls)
calls = calls.clusterCallsByCohort(gamma=args.gamma, cohort_field="cohort", cophenetic_cutoff=args.cophenetic_cutoff)
#clean up calls table
del calls.calls["cnvrID_ESP"]
calls = CallTable(calls.calls.rename(columns={'cnvr_frequency_HSCR': 'cnvr_frequency', 'cnvrID_HSCR': 'cnvrID'}))
# filter for original cohort and save
calls.filter(lambda x: x["cohort"] == args.cohort).save(args.outfile)
from conifertools import CallTable
import argparse
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--call_files",
nargs="+",
action="store",
required=True)
parser.add_argument("--outfile", action="store", required=True)
parser.add_argument("--cols",
nargs="+",
action="store",
default=[],
required=False)
args = parser.parse_args()
calls = CallTable(args.call_files)
if len(args.cols) > 0:
calls.calls[args.cols]\
.sort(["chromosome", "start"])\
.to_csv(args.outfile, sep="\t")
else:
calls.calls\
.sort(["chromosome", "start"])\
.to_csv(args.outfile, sep="\t")
