def export_tsv(variants, target, samples_selection, fields):
"""Write the selected fields of each variants on a line, with a header.
:param target: a writable object - an HTTPResponse in our case.
:param fields: list of field names (from Variant data model).
"""
for f in EXCEPT_FIELDS:
if f in fields:
fields.remove(f)
sample_names = [s.name for s in samples_selection if s.active]
writer = csv.writer(target, delimiter='\t')
writer.writerow([COL_NAMES.get(f, capitalize(f)) for f in fields])
gts_map = {(0,0):'0/0', (1,0):'1/0', (0,1):'0/1', (1,1):'1/1', (None,None):'./.'}
db = variants.db
exp = [expose_variant_full(v, samples_selection) for v in variants]
exp = annotate_variants(exp, db)
for v in exp:
info = []
for field in fields:
val = v[field]
if field == 'genotypes_index':
assert len(sample_names) == len(val), "{} samples but {} genotypes".format(len(sample_names), len(val))
couples = ['{}:{}'.format(s,gts_map[tuple(g)]) for s,g in zip(sample_names, val)]
info.append(','.join(c for c in couples))
elif isinstance(val, (list, tuple)):
info.append(','.join(val))
else:
info.append(val)
writer.writerow(info)
def export_tsv(variants, target, samples_selection, fields):
"""Write the selected fields of each variants on a line, with a header.
:param target: a writable object - an HTTPResponse in our case.
:param fields: list of field names (from Variant data model).
"""
for f in EXCEPT_FIELDS:
if f in fields:
fields.remove(f)
sample_names = [s.name for s in samples_selection if s.active]
writer = csv.writer(target, delimiter='\t')
writer.writerow([COL_NAMES.get(f, capitalize(f)) for f in fields])
gts_map = {
(0, 0): '0/0',
(1, 0): '1/0',
(0, 1): '0/1',
(1, 1): '1/1',
(None, None): './.'
}
db = variants.db
exp = [expose_variant_full(v, samples_selection) for v in variants]
exp = annotate_variants(exp, db)
for v in exp:
info = []
for field in fields:
if field not in v:
continue
else:
val = v[field]
if field == 'genotypes_index':
assert len(sample_names) == len(
val), "{} samples but {} genotypes".format(
len(sample_names), len(val))
couples = [
'{}:{}'.format(s, gts_map[tuple(g)])
for s, g in zip(sample_names, val)
]
info.append(','.join(c for c in couples))
elif isinstance(val, (list, tuple)):
info.append(','.join(val))
else:
info.append(val)
writer.writerow(info)
def expose(self):
"""Return a dict exposing variants, filters, stats etc. to be sent to the view."""
t1 = time()
filter_result = self.apply_all_filters()
t2 = time()
var = filter_result.variants
stat = self.stats.make_stats(filter_result.ids)
t3 = time()
var = [expose_variant_full(v, self.ss) for v in var]
t4 = time()
var = annotate_variants(var, self.db)
t5 = time()
logging.info("Apply/Stats/Expose/Annotate: {:.3f}s {:.3f}s {:.3f}s {:.3f}s".format(t2-t1, t3-t2, t4-t3, t5-t4))
# TODO? How can one sort wrt. these fields?
#if self.sort.key is not None and self.sort.key not in VARIANT_FIELDS:
# self.sort.sort_dict(var, inplace=True)
response = {'variants': var}
response["filters"] = [str(x) for x in self.fc.list]
response["nfound"] = stat.total_count
response["stats"] = stat.expose()
return response
def expose(self):
"""Return a dict exposing variants, filters, stats etc. to be sent to the view."""
t1 = time()
filter_result = self.apply_all_filters()
t2 = time()
var = filter_result.variants
stat = self.stats.make_stats(filter_result.ids)
t3 = time()
var = [expose_variant_full(v, self.ss) for v in var]
t4 = time()
var = annotate_variants(var, self.db)
t5 = time()
logging.info(
"Apply/Stats/Expose/Annotate: {:.3f}s {:.3f}s {:.3f}s {:.3f}s".
format(t2 - t1, t3 - t2, t4 - t3, t5 - t4))
# TODO? How can one sort wrt. these fields?
#if self.sort.key is not None and self.sort.key not in VARIANT_FIELDS:
# self.sort.sort_dict(var, inplace=True)
response = {'variants': var}
response["filters"] = [str(x) for x in self.fc.list]
response["nfound"] = stat.total_count
response["stats"] = stat.expose()
return response