def post_minimap2_processing(ref='cogent.fa',
sam='in.trimmed.fa.sam',
output_prefix='cogent2',
seqrecs=[]):
good_for = defaultdict(lambda: [])
reader = BioReaders.GMAPSAMReader(sam,
True,
query_len_dict=dict(((r.id, len(r.seq))
for r in seqrecs)))
for r in reader:
if r.sID == '*': continue # not mapped
assert r.sID.startswith('path') # chr should be path0, path1, etc
assert 0 < r.qCoverage <= 1
assert 0 < r.identity <= 1
if r.qCoverage >= 0.98 and r.identity >= 0.98:
good_for[r.qID].append(int(r.sID[4:]))
touse = []
if len(good_for) == 0:
log.warning(
"[BUG] good_for in post_minimap2_processing is empty. Probably from cycles. CHECK!"
)
else:
N = max(max(v) for v in good_for.itervalues()) + 1
try:
prob = make_into_lp_problem(good_for.items(), N, add_noise=False)
prob.solve()
except:
prob = make_into_lp_problem(good_for.items(), N, add_noise=True)
prob.solve()
for v in prob.variables():
log.debug("{0} = {1}".format(v.name, v.varValue))
if v.varValue == 1: touse.append(int(v.name))
with open(output_prefix + '.fa', 'w') as f:
for r in SeqIO.parse(open(ref), 'fasta'):
if int(r.id[4:]) in touse:
f.write(">{0}\n{1}\n".format(r.id, r.seq))
# if there are some sequences that didn't map (possibly from cycles)
# then just use THEMSELVES
fake_path_i = max(touse) + 1 if len(touse) >= 1 else 0
for r in seqrecs:
if r.id not in good_for:
log.warning(
"[BUG] {0} is not fully mapped to cogent in minimap2. \
Likely cycle issues. Use itself in output.".format(r.id))
f.write(">path{0}\n{1}\n".format(fake_path_i, r.seq))
fake_path_i += 1
def post_gmap_processing(db_name='cogent', gff_filename='in.trimmed.fa.gff', output_prefix='cogent2', seqrecs=[]):
good_for = defaultdict(lambda: [])
reader = GFF.gmapGFFReader(gff_filename)
for r in reader:
assert r.chr.startswith('path') # chr should be path0, path1, etc
if r.coverage >= 98.: good_for[r.seqid].append(int(r.chr[4:]))
touse = []
if len(good_for) == 0:
log.warning("[BUG] good_for in post_gmap_processing is empty. Probably from cycles. CHECK!")
else:
N = max(max(v) for v in good_for.itervalues())+1
prob = make_into_lp_problem(good_for.items(), N)
prob.solve()
for v in prob.variables():
log.debug("{0} = {1}".format(v.name, v.varValue))
if v.varValue == 1: touse.append(int(v.name))
with open(output_prefix + '.fa', 'w') as f:
for r in SeqIO.parse(open(db_name + '.fa'),'fasta'):
if int(r.id[4:]) in touse:
f.write(">{0}\n{1}\n".format(r.id, r.seq))
# if there are some sequences that didn't map (possibly from cycles)
# then just use THEMSELVES
fake_path_i = max(touse)+1 if len(touse) >= 1 else 0
for r in seqrecs:
if r.id not in good_for:
log.warning("[BUG] {0} is not fully mapped to cogent in GMAP. \
Likely cycle issues. Use itself in output.".format(r.id))
f.write(">path{0}\n{1}\n".format(fake_path_i, r.seq))
fake_path_i += 1
def post_gmap_processing(db_name='cogent', gff_filename='in.trimmed.fa.gff', output_prefix='cogent2', seqrecs=[]):
good_for = defaultdict(lambda: [])
reader = GFF.gmapGFFReader(gff_filename)
for r in reader:
assert r.chr.startswith('path') # chr should be path0, path1, etc
if r.coverage >= 98.: good_for[r.seqid].append(int(r.chr[4:]))
touse = []
if len(good_for) == 0:
log.warning("[BUG] good_for in post_gmap_processing is empty. Probably from cycles. CHECK!")
else:
N = max(max(v) for v in good_for.itervalues())+1
prob = make_into_lp_problem(good_for.items(), N)
prob.solve()
for v in prob.variables():
log.debug("{0} = {1}".format(v.name, v.varValue))
if v.varValue == 1: touse.append(int(v.name))
with open(output_prefix + '.fa', 'w') as f:
for r in SeqIO.parse(open(db_name + '.fa'),'fasta'):
if int(r.id[4:]) in touse:
f.write(">{0}\n{1}\n".format(r.id, r.seq))
# if there are some sequences that didn't map (possibly from cycles)
# then just use THEMSELVES
fake_path_i = max(touse)+1 if len(touse) >= 1 else 0
for r in seqrecs:
if r.id not in good_for:
log.warning("[BUG] {0} is not fully mapped to cogent in GMAP. \
Likely cycle issues. Use itself in output.".format(r.id))
f.write(">path{0}\n{1}\n".format(fake_path_i, r.seq))
fake_path_i += 1