chain_file = args.chain
in_file = args.in_gff
out_file = args.out_gff
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_gff_file(mapTree, in_file, out_file, cstyle=args.cstyle)
elif command == 'wig':
chain_file = args.chain
in_file = args.in_wig
out_file = args.out_wig
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_wig_file(mapTree,
in_file,
out_file,
targetChromSizes,
in_format='wiggle',
cstyle=args.cstyle)
elif command == 'bigwig':
chain_file = args.chain
in_file = args.in_bw
out_file = args.out_bw
# check bigwig file
try:
bw = pyBigWig.open(in_file)
except:
print("\nPlease check if \"%s\" is in bigWig format!\n" %
in_file,
file=sys.stderr)
sys.exit(0)
elif len(sys.argv) == 5:
chain_file = sys.argv[2]
in_file = sys.argv[3]
out_file = sys.argv[4]
(mapTree, targetChromSizes, sourceChromSizes) = read_chain_file(chain_file)
crossmap_gff_file(mapTree, in_file, out_file)
else:
gff_help()
sys.exit(0)
elif sys.argv[1].lower() == 'wig':
if len(sys.argv) == 5:
chain_file = sys.argv[2]
in_file = sys.argv[3]
out_file = sys.argv[4]
(mapTree, targetChromSizes, sourceChromSizes) = read_chain_file(chain_file)
crossmap_wig_file(mapTree, in_file, out_file, targetChromSizes, in_format = 'wiggle')
else:
wig_help()
sys.exit(0)
elif sys.argv[1].lower() == 'bigwig':
if len(sys.argv) == 5:
chain_file = sys.argv[2]
in_file = sys.argv[3]
try:
bw = pyBigWig.open(in_file)
except:
print ("\nPlease check if \"%s\" is in bigWig format!\n" % in_file, file=sys.stderr)
sys.exit(0)
out_file = sys.argv[4]