#!/usr/bin/env python3 from checkbed.Checkcoll import Checkcoll import sys x = Checkcoll(sys.argv[1]) x.bedinfo()
#!/usr/bin/env python3
from checkbed.Checkcoll import Checkcoll
import sys
helpmsg = """
Description:
Generates bim and fam files for collapsed bed files
Usage:
bimfamgen BED_FILE (original)
"""
if "-h" in sys.argv or "--help" in sys.argv:
print(helpmsg)
exit(0)
if len(sys.argv) == 2:
x = Checkcoll(sys.argv[1])
x.bimfamgen()
else:
print(helpmsg)
raise Exception("Arguments invalid!")
from checkbed.Checkcoll import Checkcoll
import sys
helpmsg = """
Description:
Sample some SNPs out of each of the collapsed bed files, and check if they are correct
Usage:
checkcoll BED_FILE NCHECK_EACH
Commandline Arguments:
BED_FILE: .bed file path (original, not the collapsed bed files)
NCHECK_EACH: how many SNPs to check for each collapsed bed file?
"""
if "-h" in sys.argv or "--help" in sys.argv:
print(helpmsg)
exit(0)
x = Checkcoll(sys.argv[1])
if len(sys.argv) == 3:
if not sys.argv[2].isdigit():
print(helpmsg)
raise Exception("Wrong argument, NCHECK_EACH must be a positive integer!")
x.checkall(int(sys.argv[2]))
elif len(sys.argv) == 2:
x.checkall()
else:
print(helpmsg)
raise Exception("Arguments invalid!")