def assemble_jca(readstream,
memory,
maxfpr=0.01,
collapse=True,
kmers_to_ignore=set(),
logstream=sys.stderr):
print('[kevlar::assemble::jca] loading reads', file=logstream)
countgraph = None
variants = kevlar.VariantSet()
for record in readstream:
for kmer in record.ikmers:
variants.add_kmer(kmer.sequence, record.name)
if countgraph is None:
ksize = len(kmer.sequence)
countgraph = khmer.Countgraph(ksize, memory / 4, 4)
countgraph.consume(record.sequence)
fpr = kevlar.sketch.estimate_fpr(countgraph)
msg = '[kevlar::assemble::jca] done loading reads'
msg += ', {:d} distinct k-mers stored'.format(countgraph.n_unique_kmers())
msg += '; estimated false positive rate is {:1.3f}'.format(fpr)
if fpr > maxfpr:
msg += ' (FPR too high, bailing out!!!)'
raise kevlar.sketch.KevlarUnsuitableFPRError(msg)
print(msg, file=logstream)
asm = khmer.JunctionCountAssembler(countgraph)
for kmer in variants.kmers:
if kmer in kmers_to_ignore:
continue
contigs = asm.assemble(kmer)
for contig in contigs:
if hasattr(contig, 'decode'):
contig = contig.decode()
if contig == '':
print(' WARNING: no assembly found for k-mer',
kmer,
file=args.logfile)
continue
variants.add_contig(contig, kmer)
print(' {:d} linear paths'.format(variants.ncontigs), file=logstream)
if collapse:
print('[kevlar::assemble::jca] Collapsing contigs', file=logstream)
variants.collapse()
print(' {:d} collapsed contigs'.format(variants.ncontigs),
file=logstream)
for n, contigdata in enumerate(variants, 1):
contig, contigrc, kmers, reads = contigdata
contigname = 'contig{:d}:length={:d}:nkmers={:d}:nreads={:d}'.format(
n, len(contig), len(kmers), len(reads))
contig = screed.Record(name=contigname, sequence=contig)
yield contig
def test_beginning_to_end_across_tip(self, right_tip_structure):
# assemble entire contig, ignoring branch point b/c of labels
graph, contig, L, HDN, R, tip = right_tip_structure
asm = khmer.JunctionCountAssembler(graph)
asm.consume(contig)
asm.consume(contig)
asm.consume(contig)
path = asm.assemble(contig[:K])
print('P:', path[0])
print('T:', tip)
print('C:', contig)
assert len(path) == 1, "there should only be one path"
path = path[0] # @CTB
assert len(path) == len(contig)
assert utils._equals_rc(path, contig)
def main():
p = build_counting_args(descr='Streaming assembly with tracking info')
p.add_argument('fastq_files', nargs='+')
p.add_argument('--prefix', default='transcriptome')
args = p.parse_args()
cg = create_countgraph(args)
asm = khmer.JunctionCountAssembler(cg)
tr_fn = '{0}.transcripts.fa'.format(args.prefix)
orf_fn = '{0}.orfs.fa'.format(args.prefix)
stats_fn = '{0}.stats.fa'.format(args.prefix)
with open(tr_fn, 'w') as tr_fp,\
open(orf_fn, 'w') as orf_fp,\
open(stats_fn, 'w') as stats_fp:
kept = 0
next_contig = 1
next_orf = 1
output = set()
statswriter = csv.DictWriter(
stats_fp,
delimiter=',',
fieldnames=['read_n', 'action', 'cov', 'n_junctions', 'contig_n'])
for filename in args.fastq_files:
for n, record in enumerate(screed.open(filename)):
if n and n % 10000 == 0:
print('...', n, file=sys.stderr)
if len(record.sequence) < args.ksize:
continue
cov, _, _ = cg.get_median_count(record.sequence)
if cov < 20:
kept += 1
cg.consume(record.sequence)
statswriter.writerow({
'read_n': n,
'action': 'c',
'cov': cov,
'n_junctions': None,
'contig_n': None
})
elif cov < 30:
seq, pos = cg.trim_on_abundance(record.sequence, 3)
if len(seq) < args.ksize:
continue
n_junctions = asm.consume(seq)
statswriter.writerow({
'read_n': n,
'action': 't',
'cov': cov,
'n_junctions': n_junctions,
'contig_n': None
})
elif cov == 30:
contigs = asm.assemble(record.sequence[:args.ksize])
for contig_n, contig in enumerate(contigs):
statswriter.writerow({
'read_n':
n,
'action':
'a',
'cov':
cov,
'n_junctions':
None,
'contig_n': (next_contig, contig_n)
})
tr_fp.write('>contig%d\n%s\n' % (next_contig, contig))
next_contig += 1
for t in translate(contig):
for orf_n, o in enumerate(extract_orfs(t)):
if hash(o) not in output:
new = True
output.add(hash(o))
orf_fp.write('>orf%d\n%s\n' %
(next_orf, o))
next_orf += 1
else:
new = False
else:
statswriter.writerow({
'read_n': n,
'action': 's',
'cov': cov,
'n_junctions': None,
'contig_n': None
})