def save_coverages(contigs, coverage_filename):
"""
:param contigs: A dict contig_name -> contig_id.
:param coverage_filename: The name of the dsv file.
"""
coverage_file = utils.parse_dsv(coverage_filename)
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
def add_coverages(contig_name, _coverages):
try:
contig_id = contigs.pop(contig_name)
except KeyError:
return
for i, cov in enumerate(_coverages):
db.session.add(
Coverage(value=cov, name=header[i], contig_id=contig_id))
header = fields[1:]
if not has_header:
header = ['cov_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
add_coverages(contig_name, _coverages)
for contig_name, *_coverages in coverage_file:
add_coverages(contig_name, _coverages)
db.session.commit()
def save_coverages(contigs, coverage_filename):
"""
:param contigs: A dict contig_name -> contig_id.
:param coverage_filename: The name of the dsv file.
"""
coverage_file = utils.parse_dsv(coverage_filename)
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
def add_coverages(contig_name, _coverages):
try:
contig_id = contigs.pop(contig_name)
except KeyError:
return
for i, cov in enumerate(_coverages):
db.session.add(Coverage(value=cov, name=header[i], contig_id=contig_id))
header = fields[1:]
if not has_header:
header = ['cov_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
add_coverages(contig_name, _coverages)
for contig_name, *_coverages in coverage_file:
add_coverages(contig_name, _coverages)
db.session.commit()
def save_bin_set_job(name, assembly_id, filename=None):
assembly = Assembly.query.get(assembly_id)
bin_set = BinSet(name=name,
color=randcol.generate(luminosity='dark')[0],
submit_date=datetime.utcnow(),
assembly=assembly)
db.session.add(bin_set)
db.session.flush()
# Query the contigs from the db to dict contig-name -> contig object
query = assembly.contigs.options(load_only('name'))
contigs = {c.name: c for c in query.all()}
notfound = []
if filename:
# Dict: bin -> contigs
bins = defaultdict(list)
for contig_name, bin_name in utils.parse_dsv(filename):
if contig_name in contigs:
bins[bin_name].append(contig_name)
else:
notfound.append(contig_name)
for bin_name, bin_contigs in bins.items():
notfound.extend([c for c in bin_contigs if c not in contigs])
bin_contigs = [contigs.pop(c) for c in bin_contigs]
Bin(name=bin_name, color=randcol.generate(luminosity='dark')[0],
bin_set_id=bin_set.id, contigs=bin_contigs)
os.remove(filename)
# Create a bin for the unbinned contigs.
bin = Bin(name='unbinned', color='#939393', bin_set_id=bin_set.id,
contigs=list(contigs.values()), unbinned=True)
db.session.add(bin)
db.session.flush()
for bin in bin_set.bins:
bin.recalculate_values()
db.session.commit()
return {
'assembly': assembly.id,
'binSet': bin_set.id,
'missing': list(contigs.keys()),
'notfound': notfound
}
def read_coverages(filename):
coverage_file = utils.parse_dsv(filename)
coverages = {}
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
if has_header:
samples = fields[1:]
else:
samples = ['sample_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
coverages[contig_name] = {samples[i]: _coverages[i] for i, _ in enumerate(samples)}
for contig_name, *_coverages in coverage_file:
coverages[contig_name] = {samples[i]: _coverages[i] for i, _ in enumerate(samples)}
os.remove(filename)
return samples, coverages
def post(self, contigset_id):
contigset = user_contigset_or_404(contigset_id)
args = self.reqparse.parse_args()
bin_file = tempfile.NamedTemporaryFile(delete=False)
args.bins.save(bin_file)
bin_file.close()
# Dict: bin -> contigs
bins = defaultdict(list)
for contig_name, bin_name in utils.parse_dsv(bin_file.name):
bins[bin_name].append(contig_name)
bin_objects = []
contigs = {c.name: c for c in contigset.contigs}
for bin_name, bin_contigs in bins.items():
bin_contigs = [contigs.pop(c) for c in bin_contigs]
bin = Bin(name=bin_name, color=self.randcol.generate()[0],
contigs=bin_contigs)
bin.recalculate_values()
bin_objects.append(bin)
# Create a bin for the unbinned contigs.
bin = Bin(name='unbinned', color='#939393',
contigs=list(contigs.values()))
bin.recalculate_values()
bin_objects.append(bin)
binset = Binset(name=args.name, color=self.randcol.generate()[0],
bins=bin_objects, contigset=contigset)
os.remove(bin_file.name)
db.session.add(binset)
db.session.commit()
return {'id': binset.id, 'name': binset.name, 'color': binset.color,
'bins': [bin.id for bin in binset.bins], 'contigset': contigset.id}