def load_pairs_fixture(self, fixture_name):
pairs = []
with open( u.get_fixture_path(fixture_name), 'r' ) as f:
for line in f:
if not re.match("\s*#", line): # if line doesn't start with #
pairs.append(line.rstrip("\n\r").split("\t"))
return pairs
def load_pairs_fixture(self, fixture_name):
pairs = []
with open(u.get_fixture_path(fixture_name), 'r') as f:
for line in f:
if not re.match("\s*#", line): # if line doesn't start with #
pairs.append(line.rstrip("\n\r").split("\t"))
return pairs
def setUp(self):
utils.build_ref_index()
self.aligner = BwaAligner510()
self.aligner.reference = utils.reference
self.aligner.hit_visitor = type(self).SimpleVisitor()
self.pairs = []
with open(utils.get_fixture_path("pairs.txt")) as f:
for line in f:
if not line.startswith("#"): # leave #-lines for comments
self.pairs.append(line.rstrip("\r\n").split("\t"))
def setUp(self):
self.gap_opts = FakeOpts()
self.reference = FakeReference()
# To fake having a reference, we have to overwrite the bwa.get_seq_id function
# called by BwaMapping so that it'll use our FakeReference instead of the real one.
bwa.get_seq_id = lambda bns, pos, len: self.reference.get_seq_id(bns, pos, len)
# now create the hits
# With have a file with 10 serialized dictionaries containing values most fields of
# the bwa_seq_t struct. The items are in the order read1, mate1, read2, mate2, ...
with open(utils.get_fixture_path("hit_wrapper_hits.pickle")) as f:
hits_data = pickle.load(f) # load an array of dictionaries
self.bwa_seqs = map(utils.build_bwa_seq_t, hits_data)
# finally, create the BwaMapping objects for each bwa_seq_t
self.hits = []
for s1, s2 in izip( self.bwa_seqs[0::2], self.bwa_seqs[1::2] ):
self.hits.append( BwaMapping(self.gap_opts, self.reference, s1, s2) )
self.hits.append( BwaMapping(self.gap_opts, self.reference, s2, s1) )
def setUp(self):
self.gap_opts = FakeOpts()
self.reference = FakeReference()
# To fake having a reference, we have to overwrite the bwa.get_seq_id function
# called by BwaMapping so that it'll use our FakeReference instead of the real one.
bwa.get_seq_id = lambda bns, pos, len: self.reference.get_seq_id(bns, pos, len)
# now create the hits
# With have a file with 10 serialized dictionaries containing values most fields of
# the bwa_seq_t struct. The items are in the order read1, mate1, read2, mate2, ...
with open(utils.get_fixture_path("hit_wrapper_hits.pickle")) as f:
hits_data = pickle.load(f) # load an array of dictionaries
self.bwa_seqs = map(utils.build_bwa_seq_t, hits_data)
# finally, create the BwaMapping objects for each bwa_seq_t
self.hits = []
for s1, s2 in izip( self.bwa_seqs[0::2], self.bwa_seqs[1::2] ):
self.hits.append( BwaMapping(self.gap_opts, self.reference, s1, s2) )
self.hits.append( BwaMapping(self.gap_opts, self.reference, s2, s1) )