def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
if options['line_regexp']:
p = re.compile('^' + options.args.pop(0) + '$')
else:
p = re.compile(options.args.pop(0))
sys.argv[1:] = options.args
# organize the main job...
# check function
if options['inverse']:
check = lambda p, header: p.search(header) is None
else:
check = lambda p, header: p.search(header) is not None
# parse input
for header, sequence in fasta.reader(fileinput.input()):
if check(p, header):
fasta.writer(header, sequence, sys.stdout)
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
# organize the main job...
sequences = list(fasta.reader(fileinput.input()))
n = len(sequences)
l = len(sequences[0][1])
# check that all sequences are of the same length
if not all(len(sequence) for header, sequence in sequences):
raise ValueError("All sequence are not of the same length.")
# write nuc file header
sys.stdout.write(" {} {}\n".format(n, l))
# write sequence lines
for header, sequence in sequences:
if len(header) > 30:
raise ValueError("Sequence header length must not exceed 30")
nuc_writer(header, sequence, sys.stdout)
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
sys.argv[1:] = options.args
# organize the main job...
for name, sequence in fasta.reader(fileinput.input()):
fasta.writer(name, sequence[options["slice"]], sys.stdout)
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
sys.argv[1:] = options.args
# organize the main job...
# parse input
for header, sequence in fasta.reader(fileinput.input()):
sys.stdout.write("{}\t{}\n".format(header[1:], len(sequence)))
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
# get the range
r = fasta.read_range(options.args.pop(0))
sys.argv[1:] = options.args
# organize the main job...
for header, sequence in fasta.reader(fileinput.input()):
new_sequence = sequence[r]
fasta.writer(header, new_sequence, sys.stdout)
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
# get conversion table
with open(options.args.pop(0)) as f:
d = get_correspondance_table(f)
sys.argv[1:] = options.args
# organize the main job...
for header, sequence in fasta.reader(fileinput.input()):
try:
new_header = d[header]
except KeyError:
new_header = header
fasta.writer(new_header, sequence, sys.stdout)
# return 0 if everything succeeded
return 0
def main(argv=sys.argv):
# read options and remove options strings from argv (avoid option
# names and arguments to be handled as file names by
# fileinput.input().
options = Options(argv)
# get conversion table
with open(options.args.pop(0)) as f:
s = get_list(f)
sys.argv[1:] = options.args
# organize the main job...
for header, sequence in fasta.reader(fileinput.input()):
x = header.split()[0] if options['short'] else header
if x not in s:
continue
fasta.writer(header, sequence, sys.stdout)
# return 0 if everything succeeded
return 0