def test_map_index_name(self):
"""Map index sequences to names
"""
# Some test cases
from scilifelab.illumina.index_definitions import BASIC_LOOKUP
random_keys = [BASIC_LOOKUP.keys()[random.randint(0,len(BASIC_LOOKUP.keys())-1)] for n in xrange(25)]
for name in random_keys:
self.assertIn(name,map_index_name(BASIC_LOOKUP[name],0),
"Exact mapping did not return expected index name")
def test_map_index_name(self):
"""Map index sequences to names
"""
# Some test cases
from scilifelab.illumina.index_definitions import BASIC_LOOKUP
random_keys = [
BASIC_LOOKUP.keys()[random.randint(0,
len(BASIC_LOOKUP.keys()) - 1)]
for n in xrange(25)
]
for name in random_keys:
self.assertIn(name, map_index_name(BASIC_LOOKUP[name], 0),
"Exact mapping did not return expected index name")
def map_index_name(index, mismatch=0):
"""Map the index sequences to the known names, if possible. Requires the samplesheet module.
"""
names = []
for name, sequence in BASIC_LOOKUP.items():
try:
if index != sequence and hamming_distance(index, sequence) > mismatch:
continue
names.append(name)
except:
pass
return names
def map_index_name(index, mismatch=0):
"""Map the index sequences to the known names, if possible. Requires the samplesheet module.
"""
names = []
for name, sequence in BASIC_LOOKUP.items():
try:
if index != sequence and hamming_distance(index,
sequence) > mismatch:
continue
names.append(name)
except:
pass
return names