class AstretchScan_Test(unittest.TestCase):
def setUp(self):
self.esc = AstretchScan('data/hgex')
def test_itermatch(self):
assert [m for m in self.esc.itermatch('AAAAAAAA', '+')] == [] #>=10
assert [m for m in self.esc.itermatch('AAAAAAAAAA', '+')] == [(0, 10)]
assert [m for m in self.esc.itermatch('AAAACAAAAA', '+')] == [(0, 10)]
assert [m for m in self.esc.itermatch('AAAACACAAA', '+')] == []
assert [m for m in self.esc.itermatch('CCAAAAAAAA', '+')] == [(2, 10)]
assert [m for m in self.esc.itermatch('AAAAAAAACC', '+')] == [(0, 8)]
assert [m for m in self.esc.itermatch('CCCCCAAAAAAAAAACCCCC', '+')] == [(5, 15)]
assert [m for m in self.esc.itermatch('AAAAAAAACCAAAAAAAACC', '+')] == [(0, 18)]
assert [m for m in self.esc.itermatch('AAAAAAAACCCAAAAAAAACC', '+')] == [(0, 8), (11, 19)]
assert [m for m in self.esc.itermatch('TTTTTTTT', '-')] == [] #>=10
assert [m for m in self.esc.itermatch('TTTTTTTTTT', '-')] == [(0, 10)]
assert [m for m in self.esc.itermatch('TTTTCTTTTT', '-')] == [(0, 10)]
assert [m for m in self.esc.itermatch('TTTTCTCTTT', '-')] == []
assert [m for m in self.esc.itermatch('CCTTTTTTTT', '-')] == [(2, 10)]
assert [m for m in self.esc.itermatch('TTTTTTTTCC', '-')] == [(0, 8)]
assert [m for m in self.esc.itermatch('CCCCCTTTTTTTTTTCCCCC', '-')] == [(5, 15)]
assert [m for m in self.esc.itermatch('TTTTTTTTCCTTTTTTTTCC', '-')] == [(0, 18)]
assert [m for m in self.esc.itermatch('TTTTTTTTCCCTTTTTTTTCC', '-')] == [(0, 8), (11, 19)]
def setUp(self):
self.esc = AstretchScan('data/hgex')
help='Show this help message and exit.')
(options, args) = parser.parse_args(argv)
if len(args) < 2:
parser.error("genome_dir is required")
return options, args
################################################################################
if __name__ == '__main__':
options, args = process_command_line(sys.argv)
genome_dir = args[1]
assert os.path.exists(genome_dir)
outhandle = sys.stdout
if options.outfile:
outhandle = open(options.outfile, "w")
scanner = AstretchScan(genome_dir, options.f_ival)
i = 0
for chrom, start, end, strand in scanner.scan():
i += 1
outhandle.write("\t".join(map(str, [
chrom, start, end, i, 0, strand]))+"\n")
if options.outfile:
outhandle.close()