def count_kmers(
fg_genome_fp,
bg_genome_fp,
min_size,
max_size,
min_fg_bind,
max_bg_bind,
max_dimer_bp,
primer_db,
exclude_fp,
exclude_threshold,
**kwargs):
assert os.path.isfile(fg_genome_fp)
assert os.path.isfile(bg_genome_fp)
check_create_tables(primer_db)
swga.utils.mkdirp(output_dir)
kmers = []
for k in xrange(min_size, max_size + 1):
fg = swga.primers.count_kmers(k, fg_genome_fp, output_dir)
bg = swga.primers.count_kmers(k, bg_genome_fp, output_dir)
if exclude_fp:
assert os.path.isfile(exclude_fp)
ex = swga.primers.count_kmers(
k, exclude_fp, output_dir, exclude_threshold)
else:
ex = {}
# Keep kmers found in foreground, merging bg binding values, and
# excluding those found in the excluded fasta
kmers = [
primer_dict(seq, fg, bg, min_fg_bind, max_bg_bind, max_dimer_bp)
for seq in fg.viewkeys() if seq not in ex.viewkeys()
]
kmers = filter(lambda x: x != {}, kmers)
nkmers = len(kmers)
chunk_size = 199
swga.message("Writing {n} {k}-mers into db in blocks of {cs}..."
.format(n=nkmers*2, k=k, cs=chunk_size))
database.add_primers(kmers, chunk_size, add_revcomp=True)
swga.message("Counted kmers in range %d-%d" % (min_size, max_size))
def count_specific_kmers(
kmers,
fg_genome_fp,
bg_genome_fp,
primer_db,
**kwargs):
try:
# Skip primers that already exist and warn users
existing = [p.seq for p in Primer.select().where(Primer.seq << kmers)]
for p in existing:
swga.message("{} already exists in db, skipping...".format(p))
kmers = filter(lambda p: p not in existing, kmers)
except OperationalError:
# If this fails due to an OperationalError, it probably means the
# database tables haven't been created yet
check_create_tables(primer_db)
swga.utils.mkdirp(output_dir)
# Group the kmers by length to avoid repeatedly counting kmers of the same size
kmers_by_length = defaultdict(list)
for kmer in kmers:
kmers_by_length[len(kmer)].append(kmer)
for k, mers in kmers_by_length.items():
fg = swga.primers.count_kmers(k, fg_genome_fp, output_dir, 1)
bg = swga.primers.count_kmers(k, bg_genome_fp, output_dir, 1)
primers = []
for mer in mers:
try:
primers.append(primer_dict(mer, fg, bg, 0, INF, INF))
except KeyError:
swga.message(
"{} does not exist in foreground genome, skipping..."
.format(mer))
# Omitting any primers that were returned empty
# primers = filter(lambda p: p == {}, primers)
chunk_size = 199
swga.message(
"Writing {n} {k}-mers into db in blocks of {cs}..."
.format(n=len(primers), k=k, cs=chunk_size))
database.add_primers(primers, chunk_size, add_revcomp=False)
def test_add_primers(self, initdb):
'''Must add the reverse complement of a primer if requested.'''
primers = [{'seq': "AAAA"}]
database.add_primers(primers, add_revcomp=True)
assert Primer.select().where(Primer.seq == "TTTT").count() == 1
