def main():
ap = ArgumentParser()
ap.add_argument("genome", nargs=1)
args = ap.parse_args()
genome = load(args.genome[0])
codons = to_codons(genome)
shuffle(codons)
print(from_codons(codons))
def main():
ap = ArgumentParser()
ap.add_argument("genome", nargs=1)
ap.add_argument("range", help="For example 24750..24983", nargs="+")
args = ap.parse_args()
genome = load(args.genome[0])
for r in args.range:
start, end = [int(x) for x in re.split(r'[^\d+]', r) if x]
print(r)
print(fill(genome[start:end], 80))
def main():
ap = ArgumentParser()
ap.add_argument("haystacks", nargs="+")
ap.add_argument("-t", "--needle", type=str)
ap.add_argument("-v", "--verbose", action="store_true")
args = ap.parse_args()
term = args.needle.lower()
for h in args.haystacks:
genome = load(h)
n = search(genome, term, args.verbose)
print("{}: {}".format(h, n))
def main():
ap = ArgumentParser()
ap.add_argument('-n', "--newlines", action="store_true")
ap.add_argument("genome", nargs=1)
args = ap.parse_args()
genome = load(args.genome[0])
aa = convert_to_aa(genome)
if args.newlines:
for a in aa:
print(a)
else:
print(convert_to_aa(genome))
def main():
ap = ArgumentParser()
ap.add_argument("genome", nargs="+")
ap.add_argument('-s', "--shift", type=int)
args = ap.parse_args()
for fname in args.genome:
genome = cg.load(fname)
if args.shift:
genome = genome[args.shift:]
display(genome)