def test_augfastx_writer():
output = StringIO()
record = Record(
name='BasiliscusVulgarisRead84467/1',
sequence='TTAACTCTAGATTAGGGGCGTGACTTAATAAGGTGTGGGCCTAAGCGTCT',
quality='BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB',
annotations=[
KmerOfInterest(ksize=19, offset=13, abund=(12, 1, 1)),
KmerOfInterest(ksize=19, offset=15, abund=(20, 0, 1)),
],
)
kevlar.print_augmented_fastx(record, output)
record = Record(
name='BasiliscusVulgarisRead90577/2',
sequence='CTGTAATCCCAGCACTTTGGGAGGCCGAGGCAAGCAGATGATGCGGTCAG',
quality='BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB',
annotations=[
KmerOfInterest(ksize=19, offset=1, abund=(5, 7, 9)),
KmerOfInterest(ksize=19, offset=2, abund=(7, 10, 9)),
],
mates=['CAGATGTGTCTTGTGGGCAGTGCAGCGGAGAGGTGCAAATATGGGTTTGG']
)
kevlar.print_augmented_fastx(record, output)
record = Record(
name='BasiliscusVulgarisRead99037/1',
sequence='AGCACTTTGGGAGGCCGAGGCAAGCAGATGATGCGGTCAGGATTACAGAT',
quality='BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'
)
kevlar.print_augmented_fastx(record, output)
assert output.getvalue() == """@BasiliscusVulgarisRead84467/1
def dump(bamstream,
refrseqs=None,
pairmode='split',
upint=50000,
logstream=sys.stderr):
"""
Parse read alignments in BAM/SAM format.
- bamstream: open file handle to the BAM/SAM file input
- refrseqs: dictionary of reference sequences, indexed by sequence ID; if
provided, perfect matches to the reference sequence will be discarded
- strict: only keep paired end if it also lacks a perfect match to the
reference genome
- upint: update interval for progress indicator
- logstream: file handle do which progress indicator will write output
"""
bam = pysam.AlignmentFile(bamstream, 'rb')
reader = bam_paired_reader(bam)
for i, (record1, record2) in enumerate(reader, 1):
if i % upint == 0: # pragma: no cover
print('...processed', i, 'pairs of records', file=logstream)
for record in keepers(record1, record2, bam, refrseqs, pairmode):
yield Record(name=readname(record),
sequence=record.seq,
quality=record.qual)
def revcom(self):
seq = kevlar.revcom(self.read.sequence)
kmerseqrc = kevlar.revcom(self.kmerseq)
newoffset = len(seq) - self.kmer.offset - self.kmer.ksize
kmer = KmerOfInterest(self.kmer.ksize, newoffset, self.kmer.abund)
kdict = {self.kmerseq: kmer, kmerseqrc: kmer}
newread = Record(self.read.name, seq, annotations=[kmer], ikmers=kdict)
return ReadWithKmer(newread, self.kmerseq)
def record5():
return Record(
name='read5',
sequence='CTCTTCCGGCAGTCACTGTCAAGAGAGGGTGAACT',
annotations=[
KmerOfInterest(7, 15, [12, 0, 0]),
KmerOfInterest(7, 16, [13, 0, 0]),
],
)
def record2a():
return Record(
name='read2',
sequence='ACGCAAAGCTATTTACGCAA',
annotations=[
KmerOfInterest(5, 1, [15, 0, 0]),
KmerOfInterest(5, 15, [15, 0, 0]),
],
)
def record6():
return Record(
name='read6',
sequence='TCACTGTCAAGAGAGGCCTACGGATTCGGTTACTG',
annotations=[
KmerOfInterest(7, 3, [12, 0, 0]),
KmerOfInterest(7, 4, [13, 0, 0]),
],
)
def record4():
# similar to record2 but with a single nucleotide mismatch
return Record(
name='read4',
sequence='ACGCAATGCTATTTAAAACC',
annotations=[
KmerOfInterest(5, 1, [15, 0, 0]),
KmerOfInterest(5, 14, [19, 1, 0]),
],
)
def record3fix():
# reverse complement of record2
return Record(
name='read3',
sequence='GGTTTTAAATAGCTTTGCGT',
annotations=[
KmerOfInterest(5, 1, [19, 1, 0]),
KmerOfInterest(5, 14, [15, 0, 0]),
],
)
def mutate_genome(infile, mutations):
parser = parse_augmented_fastx(kevlar.open(infile, 'r'))
for record in parser:
sequence = record.sequence
if record.name in mutations:
mutlist = sorted(mutations[record.name],
key=lambda m: m.pos,
reverse=True)
sequence = mutate_sequence(sequence, mutlist)
yield Record(name=record.name, sequence=sequence)
def main(args):
contigstream = kevlar.parse_augmented_fastx(kevlar.open(args.contigs, 'r'))
outstream = kevlar.open(args.out, 'w')
localizer = localize(contigstream,
args.refr,
seedsize=args.seed_size,
delta=args.delta,
maxdiff=args.max_diff,
logstream=args.logfile)
for cutout in localizer:
record = Record(name=cutout.defline, sequence=cutout.sequence)
kevlar.sequence.write_record(record, outstream)
def picorecord4():
return Record(
name='seqname',
sequence=('TGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAGTTG'
'GAAGTGAGGTCTCAGCCTGCACAAACGAATAAATG'),
annotations=[
KmerOfInterest(25, 8, [17, 0, 0]),
KmerOfInterest(25, 7, [18, 0, 0]),
KmerOfInterest(25, 6, [18, 1, 0]),
KmerOfInterest(25, 5, [18, 1, 0]),
KmerOfInterest(25, 4, [19, 0, 0]),
],
)
def picorecord3():
return Record(
name='seq1_901428_901847_3:0:0_0:0:0_87d/1',
sequence=('TATTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAG'
'TTGGAAGTGAGGTCTCAGCCTGCACAAACGAATAAATGTAA'),
annotations=[
KmerOfInterest(25, 11, [17, 0, 0]),
KmerOfInterest(25, 10, [18, 0, 0]),
KmerOfInterest(25, 9, [18, 1, 0]),
KmerOfInterest(25, 8, [18, 1, 0]),
KmerOfInterest(25, 7, [19, 0, 0]),
],
)
def picorecord2():
return Record(
name='seq1_901428_901847_3:0:0_0:0:0_87d/1',
sequence=('TTACATTTATTCGTTTGTGCAGGCTGAGACCTCACTTCCAACTGTAATCCAAAAGCTTA'
'GTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATA'),
annotations=[
KmerOfInterest(25, 64, [19, 0, 0]),
KmerOfInterest(25, 65, [18, 1, 0]),
KmerOfInterest(25, 66, [18, 1, 0]),
KmerOfInterest(25, 67, [18, 0, 0]),
KmerOfInterest(25, 68, [17, 0, 0]),
],
)
def picorecord1():
return Record(
name='seq1_901350_901788_1:0:0_0:0:0_21ca1/2',
sequence=('GTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATATTTTCTCATAGTTTTGAC'
'AAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGA'),
annotations=[
KmerOfInterest(25, 5, [19, 0, 0]),
KmerOfInterest(25, 6, [18, 1, 0]),
KmerOfInterest(25, 7, [18, 1, 0]),
KmerOfInterest(25, 8, [18, 0, 0]),
KmerOfInterest(25, 9, [17, 0, 0]),
],
)
def test_align_mates():
mate_seqs = kevlar.open(data_file('minitrio/novel-mates.fastq.gz'), 'r')
record = Record(
name='bogusread',
sequence='NNNNN',
mates=[r.sequence for r in kevlar.parse_augmented_fastx(mate_seqs)]
)
refrfile = data_file('minitrio/refr.fa')
kevlar.reference.autoindex(refrfile)
positions = list(kevlar.call.align_mates(record, refrfile))
seqids = set([seqid for seqid, start, end in positions])
coords = sorted([(start, end) for seqid, start, end in positions])
print('DEBUG', coords, file=sys.stderr)
assert seqids == set(['seq1'])
assert coords == [
(45332, 45432), (45377, 45477), (45393, 45493), (45428, 45528),
(45440, 45540), (45447, 45547), (46092, 46192), (46093, 46193),
(46099, 46199), (46127, 46227), (46131, 46231), (46146, 46246),
(46148, 46248), (48025, 48125), (48035, 48135),
]
def record1fix():
return Record(
name='read1',
sequence='GCTGCACCGATGTACGCAAA',
annotations=[KmerOfInterest(5, 14, [15, 0, 0])],
)