def check_kmer_freq_in_read_pair(read1, read2, minkmer, debugstream=None):
"""
Check interesting k-mer frequence in each read.
When calculating offset between a pair of reads, do not use any interesting
k-mers that occur multiple times in either read.
"""
maxkmer = kevlar.revcom(minkmer)
matches1 = [
k for k in read1.ikmers
if kevlar.same_seq(k.sequence, minkmer, maxkmer)
]
matches2 = [
k for k in read2.ikmers
if kevlar.same_seq(k.sequence, minkmer, maxkmer)
]
nmatches1 = len(matches1)
nmatches2 = len(matches2)
assert nmatches1 > 0 and nmatches1 > 0, (nmatches1, nmatches2)
if nmatches1 > 1 or nmatches2 > 1:
if debugstream:
message = (
'stubbornly refusing to calculate offset bewteen {:s} and '
'{:s}; interesting k-mer {:s} occurs multiple times'.format(
read1.name, read2.name, minkmer))
print('[kevlar::overlap] INFO', message, file=debugstream)
return None, None
kmer1 = matches1[0]
kmer2 = matches2[0]
return kmer1, kmer2
def test_allocate_sketch_graphy(count, smallcount):
sequence = 'AATCAACGCTTCTTAATAGGCATAGTGTCTCTGCTGCGCATGGACGTGCCATAGCCACTACT'
kmer = 'GCATAGTGTCTCTGCTGCGCA'
sketch = kevlar.sketch.allocate(21, 1e4, 4, count, True, smallcount)
sketch.consume(sequence)
sketch.get(kmer) == 1
kmer_hash = sketch.hash(kmer)
assert kevlar.same_seq(sketch.reverse_hash(kmer_hash), kmer)
def test_pico(picorecord1, picorecord2, picorecord3):
pair1 = ReadPair(picorecord1, picorecord2, 'TTTTTTGTTTCCCAAAGTAAGGCTG')
assert pair1.offset == 59
assert pair1.head.read.name == 'seq1_901428_901847_3:0:0_0:0:0_87d/1'
print(pair1.mergedseq)
pair2 = ReadPair(picorecord1, picorecord3, 'TTTTTTGTTTCCCAAAGTAAGGCTG')
assert pair2.offset == 59
assert pair2.head.read.name == 'seq1_901428_901847_3:0:0_0:0:0_87d/1'
print(pair2.mergedseq)
assert kevlar.same_seq(pair1.mergedseq, pair2.mergedseq)
def test_pico_offset(picorecord1, picorecord2, picorecord3):
pair = kevlar.overlap.calc_offset(picorecord1, picorecord2,
'TTTTTTGTTTCCCAAAGTAAGGCTG')
assert pair.offset == 59
assert pair.head.name == 'seq1_901350_901788_1:0:0_0:0:0_21ca1/2'
assert pair.swapped is False
contig = kevlar.assemble.merge_pair(pair)
print(contig)
pair = kevlar.overlap.calc_offset(picorecord1, picorecord3,
'TTTTTTGTTTCCCAAAGTAAGGCTG')
assert pair.offset == 59
assert pair.head.name == 'seq1_901350_901788_1:0:0_0:0:0_21ca1/2'
assert pair.swapped is True
newcontig = kevlar.assemble.merge_pair(pair)
print(newcontig)
assert kevlar.same_seq(contig, newcontig)
def test_pico_contains(picorecord3, picorecord4):
pair = ReadPair(picorecord3, picorecord4, 'CACTCAGCCTTACTTTGGGAAACAA')
print(pair.mergedseq)
assert kevlar.same_seq(pair.mergedseq, picorecord3.sequence)