def record5():
return screed.Record(
name='read5',
sequence='CTCTTCCGGCAGTCACTGTCAAGAGAGGGTGAACT',
ikmers=[
KmerOfInterest('CTGTCAA', 15, [12, 0, 0]),
KmerOfInterest('TGTCAAG', 16, [13, 0, 0]),
],
)
def record6():
return screed.Record(
name='read6',
sequence='TCACTGTCAAGAGAGGCCTACGGATTCGGTTACTG',
ikmers=[
KmerOfInterest('CTGTCAA', 3, [12, 0, 0]),
KmerOfInterest('TGTCAAG', 4, [13, 0, 0]),
],
)
def record2a():
return screed.Record(
name='read2',
sequence='ACGCAAAGCTATTTACGCAA',
ikmers=[
KmerOfInterest('CGCAA', 1, [15, 0, 0]),
KmerOfInterest('CGCAA', 15, [15, 0, 0]),
],
)
def record4():
# similar to record2 but with a single nucleotide mismatch
return screed.Record(
name='read4',
sequence='ACGCAATGCTATTTAAAACC',
ikmers=[
KmerOfInterest('CGCAA', 1, [15, 0, 0]),
KmerOfInterest('AAAAC', 14, [19, 1, 0]),
],
)
def record3():
# reverse complement of record2
return screed.Record(
name='read3',
sequence='GGTTTTAAATAGCTTTGCGT',
ikmers=[
KmerOfInterest('GTTTT', 1, [19, 1, 0]),
KmerOfInterest('TTGCG', 14, [15, 0, 0]),
],
)
def record10():
return screed.Record(
name='read10',
sequence=('CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCT'),
ikmers=[
KmerOfInterest('TCCCCACCCGGATACTT', 4, [28, 0, 0]),
KmerOfInterest('CCCCACCCGGATACTTG', 5, [26, 0, 0]),
KmerOfInterest('CCCGGATACTTGAAGCA', 10, [21, 0, 0]),
],
)
def record9():
return screed.Record(
name='read9',
sequence=('AGCAAGGCGCTCGCGTCAACGAAGTGAGCTCCCGTGGTCTTGAGTTATCG'
'CCTCACATAC'),
ikmers=[
KmerOfInterest('AGCAAGGCGCTCGCGTC', 0, [25, 0, 0]),
KmerOfInterest('GCAAGGCGCTCGCGTCA', 1, [39, 0, 0]),
KmerOfInterest('GTTATCGCCTCACATAC', 42, [15, 1, 1]),
KmerOfInterest('AGTTATCGCCTCACATA', 43, [15, 1, 0]),
],
)
def record8():
return screed.Record(
name='read8',
sequence=('GTATGTGAGGCGATAACTCAAGACCACGGGAGCTCACTTCGTTGACGCGA'
'GCGCCTTGCT'),
ikmers=[
KmerOfInterest('GTATGTGAGGCGATAAC', 0, [15, 1, 0]),
KmerOfInterest('TATGTGAGGCGATAACT', 1, [15, 1, 1]),
KmerOfInterest('TGACGCGAGCGCCTTGC', 42, [39, 0, 0]),
KmerOfInterest('GACGCGAGCGCCTTGCT', 43, [25, 0, 0]),
],
)
def picorecord3():
return screed.Record(
name='seq1_901428_901847_3:0:0_0:0:0_87d/1',
sequence=('TATTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAG'
'TTGGAAGTGAGGTCTCAGCCTGCACAAACGAATAAATGTAA'),
ikmers=[
KmerOfInterest('CAGCCTTACTTTGGGAAACAAAAAA', 11, [17, 0, 0]),
KmerOfInterest('TCAGCCTTACTTTGGGAAACAAAAA', 10, [18, 0, 0]),
KmerOfInterest('CTCAGCCTTACTTTGGGAAACAAAA', 9, [18, 1, 0]),
KmerOfInterest('ACTCAGCCTTACTTTGGGAAACAAA', 8, [18, 1, 0]),
KmerOfInterest('CACTCAGCCTTACTTTGGGAAACAA', 7, [19, 0, 0]),
],
)
def picorecord2():
return screed.Record(
name='seq1_901428_901847_3:0:0_0:0:0_87d/1',
sequence=('TTACATTTATTCGTTTGTGCAGGCTGAGACCTCACTTCCAACTGTAATCCAAAAGCTTA'
'GTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATA'),
ikmers=[
KmerOfInterest('TTTTTTGTTTCCCAAAGTAAGGCTG', 64, [19, 0, 0]),
KmerOfInterest('TTTTTGTTTCCCAAAGTAAGGCTGA', 65, [18, 1, 0]),
KmerOfInterest('TTTTGTTTCCCAAAGTAAGGCTGAG', 66, [18, 1, 0]),
KmerOfInterest('TTTGTTTCCCAAAGTAAGGCTGAGT', 67, [18, 0, 0]),
KmerOfInterest('TTGTTTCCCAAAGTAAGGCTGAGTG', 68, [17, 0, 0]),
],
)
def picorecord1():
return screed.Record(
name='seq1_901350_901788_1:0:0_0:0:0_21ca1/2',
sequence=('GTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATATTTTCTCATAGTTTTGAC'
'AAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGA'),
ikmers=[
KmerOfInterest('TTTTTTGTTTCCCAAAGTAAGGCTG', 5, [19, 0, 0]),
KmerOfInterest('TTTTTGTTTCCCAAAGTAAGGCTGA', 6, [18, 1, 0]),
KmerOfInterest('TTTTGTTTCCCAAAGTAAGGCTGAG', 7, [18, 1, 0]),
KmerOfInterest('TTTGTTTCCCAAAGTAAGGCTGAGT', 8, [18, 0, 0]),
KmerOfInterest('TTGTTTCCCAAAGTAAGGCTGAGTG', 9, [17, 0, 0]),
],
)
def test_ikmer_abund_after_recalc():
"""
Ensure interesting k-mer abundances are correct after recalculation.
The interesting k-mer has an advertised abundance of 28, but a true
abundance (in `counts`) of 10. The readset "validate" function should check
and correct this.
"""
read = screed.Record(
name='read1',
sequence='AAGCAGGGGTCTACATTGTCCTCGGGACTCGAGATTTCTTCGCTGT',
ikmers=[KmerOfInterest('CATTGTCCTCGGGACTC', 13, [28, 0, 0])],
)
counts = khmer.Counttable(17, 1e5, 4)
seq = 'TTCGTTCCCGAAGCAGGGGTCTACATTGTCCTCGGGACTCGAGATTTCTTCGCTGTTCCGTCCTTCA'
for _ in range(10):
counts.consume(seq)
rs = ReadSet()
rs.add(read)
assert read.ikmers[0].abund[0] == 28
rs.validate(counts, minabund=8)
assert rs.valid == (1, 1)
assert read.ikmers[0].abund[0] == 10
def record7():
return screed.Record(
name='read7',
sequence=('CAGGTCCCCACCCGGATACTTGAAGCAGGCAGCCTCAAGGTATGTGAGGC'
'GATAACTCAA'),
ikmers=[
KmerOfInterest('TCCCCACCCGGATACTT', 4, [28, 0, 0]),
KmerOfInterest('CCCCACCCGGATACTTG', 5, [26, 0, 0]),
KmerOfInterest('CCCGGATACTTGAAGCA', 10, [21, 0, 0]),
KmerOfInterest('GGTATGTGAGGCGATAA', 38, [14, 0, 0]),
KmerOfInterest('GTATGTGAGGCGATAAC', 39, [15, 1, 0]),
KmerOfInterest('TATGTGAGGCGATAACT', 40, [15, 1, 1]),
],
)
def record1():
return screed.Record(
name='read1',
sequence='GCTGCACCGATGTACGCAAA',
ikmers=[KmerOfInterest('CGCAA', 14, [15, 0, 0])],
)
def record12():
return screed.Record(
name='read12',
sequence='CCCGGATACTTGAAGCAGGCAcC',
ikmers=[KmerOfInterest('CCCGGATACTTGAAGCA', 0, [21, 0, 0])],
)
