def call(targetlist,
querylist,
match=1,
mismatch=2,
gapopen=5,
gapextend=0,
ksize=31):
"""
Wrap the `kevlar call` procedure as a generator function.
Input is the following.
- an iterable containing one or more target sequences from the reference
genome, stored as khmer or screed sequence records
- an iterable containing one or more contigs assembled by kevlar, stored as
khmer or screed sequence records
- alignment match score (integer)
- alignment mismatch penalty (integer)
- alignment gap open penalty (integer)
- alignment gap extension penalty (integer)
The function yields tuples of target sequence name, query sequence name,
and alignment CIGAR string
"""
for target in sorted(targetlist, key=lambda record: record.name):
for query in sorted(querylist, reverse=True, key=len):
cigar = kevlar.align(target.sequence, query.sequence, match,
mismatch, gapopen, gapextend)
for varcall in make_call(target, query, cigar, ksize):
yield varcall
def test_nomargin():
qfile = kevlar.open(data_file('nomargin-r-indel-contigs.augfasta'), 'r')
tfile = kevlar.open(data_file('nomargin-r-gdna.fa'), 'r')
query = next(kevlar.parse_augmented_fastx(qfile))
target = next(kevlar.parse_augmented_fastx(tfile))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert tok._cigar == tok._origcigar
def test_align():
"""Smoke test for ksw2 aligner"""
target = ('TAAATAAATATCTGGTGTTTGAGGCAAAAAGGCAGACTTAAATTCTAAATCACACCTGTGCTT'
'CCAGCACTACCTTCAAGCGCAGGTTCGAGCCAGTCAGGCAGGGTACATAAGAGTCCATTGTGC'
'CTGTATTATTTTGAGCAATGGCTAAAGTACCTTCACCCTTGCTCACTGCTCCCCCACTTCCTC'
'AAGTCTCATCGTGTTTTTTTTAGAGCTAGTTTCTTAGTCTCATTAGGCTTCAGTCACCAT')
query = ('TCTGGTGTTTGAGGCAAAAAGGCAGACTTAAATTCTAAATCACACCTGTGCTTCCAGCACTACC'
'TTCAAGCGCAGGTTCGAGCCAGTCAGGACTGCTCCCCCACTTCCTCAAGTCTCATCGTGTTTTT'
'TTTAGAGCTAGTTTCTTAGTCTCATTAGGCTTCAGTCACCATCATTTCTTATAGGAATACCA')
assert kevlar.align(target, query) == ('10D91M69D79M20I', 155)
def test_gap_center_aligned(contig, gdna, newcigar, origcigar, nblocks):
qfile = kevlar.open(data_file('cigar/' + contig), 'r')
tfile = kevlar.open(data_file('cigar/' + gdna), 'r')
query = next(kevlar.parse_augmented_fastx(qfile))
target = next(kevlar.parse_augmented_fastx(tfile))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert len(tok.blocks) == nblocks
assert tok._cigar == newcigar
assert tok._origcigar == origcigar
def align_both_strands(targetseq,
queryseq,
match=1,
mismatch=2,
gapopen=5,
gapextend=0):
cigar1, score1 = kevlar.align(targetseq, queryseq, match, mismatch,
gapopen, gapextend)
cigar2, score2 = kevlar.align(targetseq, kevlar.revcom(queryseq), match,
mismatch, gapopen, gapextend)
if score2 > score1:
cigar = cigar2
score = score2
strand = -1
else:
cigar = cigar1
score = score1
strand = 1
return cigar, score, strand
def test_gap_center_aligned():
query = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('cigar/b.contig.fa'), 'r')))
target = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('cigar/b.gdna.fa'), 'r')))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert len(tok.blocks) == 3
assert tok._cigar == '41D150M50D'
assert tok._origcigar == '41D144M50D6M'
def test_blocks(contig, gdna):
query = next(kevlar.parse_augmented_fastx(kevlar.open(contig, 'r')))
target = next(kevlar.parse_augmented_fastx(kevlar.open(gdna, 'r')))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
for block in tok.blocks:
assert block.type in ('M', 'D', 'I')
if block.type in ('M', 'D'):
assert len(block.target) == block.length
else:
assert block.target is None
if block.type in ('M', 'I'):
assert len(block.query) == block.length
else:
assert block.query is None