class TestContains(unittest.TestCase):
def setUp(self):
self.e = Elf(100)
for i in range(100):
self.e.add(str(i))
def testContains(self):
for i in range(100):
self.assert_(str(i) in self.e)
class TestAddMany(unittest.TestCase):
def setUp(self):
self.e = Elf(100)
def testAdd(self):
self.e.addmany((str(i) for i in range(100)))
for i in range(100):
self.assert_(str(i) in self.e)
def testUpdate(self):
self.e.update((str(i) for i in range(100)))
for i in range(100):
self.assert_(str(i) in self.e)
class TestSerialize(TestContains):
def setUp(self):
self.e = Elf(100)
for i in range(100):
self.e.add(str(i))
self.e.save("_t.elf")
def testSave(self):
self.assert_(os.path.exists("_t.elf"))
def testLoad(self):
e = Elf.load("_t.elf")
self.assert_("1" in e)
self.assert_("10" in e)
def tearDown(self):
os.unlink("_t.elf")
__doc__ %= sys.argv[0]
if len(sys.argv) > 2:
print sys.argv
print __doc__
sys.exit()
print >> sys.stderr, "Command: ", " ".join(sys.argv)
infile = sys.argv[1]
fp = FastQParser(infile)
for _ in fp:
pass
records = fp.rread()
print >> sys.stderr, records, "records in file ", infile
# say 1 out of 1000 is false positive.
bloom = Elf(records, error_rate=1e-3)
fp.seek(0)
checks = []
for _, seq, _, _ in fp:
if seq in bloom:
checks.append(seq)
bloom.add(seq)
# now checks contains anything that could be a duplicate according to
# the bloomfilter. for some, they were false positives.
# for actual duplicated, just choose the first, but can also sort by quality.
fp.seek(0)
checks = frozenset(checks)
print >>sys.stderr, "checking %s potential duplicates in a python set" \
% len(checks)
outfile = "%s-unique.fastq.gz" % infile.split(".")[0]
def setUp(self):
self.e = Elf(100)
def testLoad(self):
e = Elf.load("_t.elf")
self.assert_("1" in e)
self.assert_("10" in e)
def setUp(self):
self.e = Elf(100)
for i in range(100):
self.e.add(str(i))
self.e.save("_t.elf")
def setUp(self):
self.e = Elf(100)
for i in range(100):
self.e.add(str(i))
%s < in.fastq > out.unique.fastq
"""
from bloomfaster import Elf
import collections
import sys
__doc__ %= sys.argv[0]
if len(sys.argv) > 1:
print sys.argv
print __doc__
sys.exit()
records = sum(1 for _ in sys.stdin) / 2
print >>sys.stderr, records, "records in file"
# say 1 out of 1000 is false positive.
bloom = Elf(records, error_rate=1e-3)
sys.stdin.seek(0)
readline = sys.stdin.readline
checks = []
header = readline().rstrip()
while header:
seq = readline().rstrip()
if seq in bloom:
checks.append(seq)
bloom.add(seq)
header = readline().rstrip()
# now checks contains anything that could be a duplicate according to
# the bloomfilter. for some, they were false positives.
