def __getitem__(self, key):
# we cache what we can.
if key in ('het_samples', 'hom_alt_samples', 'unknown_samples',
'variant_samples', 'hom_ref_samples'):
if self.genotype_dict == {}:
self.genotype_dict = self.query._group_samples_by_genotype(self['gt_types'])
if key == 'het_samples':
return self.genotype_dict[HET]
if key == 'hom_alt_samples':
return self.genotype_dict[HOM_ALT]
if key == 'hom_ref_samples':
return self.genotype_dict[HOM_REF]
if key == 'unknown_samples':
return self.genotype_dict[UNKNOWN]
if key == 'variant_samples':
return self.genotype_dict[HET] + self.genotype_dict[HOM_ALT]
if key in self.cache:
return self.cache[key]
if key == 'info':
if 'info' not in self.cache:
self.cache['info'] = compression.unpack_ordereddict_blob(self.row['info'])
return self.cache['info']
if key not in self.query.gt_cols:
return self.row[key]
elif key in self.query.gt_cols:
if key not in self.cache:
self.cache[key] = compression.unpack_genotype_blob(self.row[key])
return self.cache[key]
raise KeyError(key)
def row_2_GeminiRow(self, row):
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
fields = OrderedDict()
for col in self.report_cols:
if col == "*":
continue
if not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = _info_dict_to_string(info)
if self.show_variant_samples or self.needs_sample_names:
het_names = self._get_variant_samples(row['variant_id'], HET)
hom_alt_names = self._get_variant_samples(row['variant_id'], HOM_ALT)
hom_ref_names = self._get_variant_samples(row['variant_id'], HOM_REF)
unknown_names = self._get_variant_samples(row['variant_id'], UNKNOWN)
variant_names = het_names | hom_alt_names
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(variant_names)
fields["HET_samples"] = \
self.variant_samples_delim.join(het_names)
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(hom_alt_names)
if self.show_families:
families = map(str, list(set([self.sample_to_sample_object[x].family_id
for x in variant_names])))
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields, variant_names, het_names, hom_alt_names,
hom_ref_names, unknown_names, info,
formatter=self.formatter)
if not all([predicate(gemini_row) for predicate in self.predicates]):
return None
if not self.for_browser:
return gemini_row
else:
return fields
def barebones_row2geminiRow(row, report_cols):
info = None
if 'info' in report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
fields = OrderedDict()
for col in report_cols:
if col == "*":
continue
if not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = _info_dict_to_string(info)
gemini_row = GeminiRow(fields, [], [], [], [], [], info)
return gemini_row
def barebones_row2geminiRow(row, report_cols):
info = None
if 'info' in report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
fields = OrderedDict()
for col in report_cols:
if col == "*":
continue
if not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = _info_dict_to_string(info)
gemini_row = GeminiRow(fields, [], [], [], [], [], info)
return gemini_row
def next(self):
"""
Return the GeminiRow object for the next query result.
"""
# we use a while loop since we may skip records based upon
# genotype filters. if we need to skip a record, we just
# throw a continue and keep trying. the alternative is to just
# recursively call self.next() if we need to skip, but this
# can quickly exceed the stack.
while (1):
try:
row = self.c.next()
except Exception as e:
self.conn.close()
raise StopIteration
gts = None
gt_types = None
gt_phases = None
gt_depths = None
gt_ref_depths = None
gt_alt_depths = None
gt_quals = None
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
if self._query_needs_genotype_info():
gts = compression.unpack_genotype_blob(row['gts'])
gt_types = \
compression.unpack_genotype_blob(row['gt_types'])
gt_phases = \
compression.unpack_genotype_blob(row['gt_phases'])
gt_depths = \
compression.unpack_genotype_blob(row['gt_depths'])
gt_ref_depths = \
compression.unpack_genotype_blob(row['gt_ref_depths'])
gt_alt_depths = \
compression.unpack_genotype_blob(row['gt_alt_depths'])
gt_quals = \
compression.unpack_genotype_blob(row['gt_quals'])
variant_samples = [
x for x, y in enumerate(gt_types)
if y == HET or y == HOM_ALT
]
variant_names = [
self.idx_to_sample[x] for x in variant_samples
]
het_samples = [x for x, y in enumerate(gt_types) if y == HET]
het_names = [self.idx_to_sample[x] for x in het_samples]
hom_alt_samples = [
x for x, y in enumerate(gt_types) if y == HOM_ALT
]
hom_alt_names = [
self.idx_to_sample[x] for x in hom_alt_samples
]
hom_ref_samples = [
x for x, y in enumerate(gt_types) if y == HOM_REF
]
hom_ref_names = [
self.idx_to_sample[x] for x in hom_ref_samples
]
unknown_samples = [
x for x, y in enumerate(gt_types) if y == UNKNOWN
]
unknown_names = [
self.idx_to_sample[x] for x in unknown_samples
]
families = map(
str,
list(
set([
self.idx_to_sample_object[x].family_id
for x in variant_samples
])))
# skip the record if it does not meet the user's genotype filter
if self.gt_filter and not eval(self.gt_filter, locals()):
continue
fields = OrderedDict()
for idx, col in enumerate(self.report_cols):
if col == "*":
continue
if not col.startswith("gt") and not col.startswith(
"GT") and not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = self._info_dict_to_string(info)
else:
# reuse the original column name user requested
# e.g. replace gts[1085] with gts.NA20814
if '[' in col:
orig_col = self.gt_idx_to_name_map[col]
val = eval(col.strip())
if type(val) in [np.int8, np.int32, np.bool_]:
fields[orig_col] = int(val)
elif type(val) in [np.float32]:
fields[orig_col] = float(val)
else:
fields[orig_col] = val
else:
# asked for "gts" or "gt_types", e.g.
if col == "gts":
fields[col] = ','.join(gts)
elif col == "gt_types":
fields[col] = \
','.join(str(t) for t in gt_types)
elif col == "gt_phases":
fields[col] = \
','.join(str(p) for p in gt_phases)
elif col == "gt_depths":
fields[col] = \
','.join(str(d) for d in gt_depths)
elif col == "gt_quals":
fields[col] = \
','.join(str(d) for d in gt_quals)
elif col == "gt_ref_depths":
fields[col] = \
','.join(str(d) for d in gt_ref_depths)
elif col == "gt_alt_depths":
fields[col] = \
','.join(str(d) for d in gt_alt_depths)
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(variant_names)
fields["HET_samples"] = \
self.variant_samples_delim.join(het_names)
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(hom_alt_names)
if self.show_families:
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields,
gts,
gt_types,
gt_phases,
gt_depths,
gt_ref_depths,
gt_alt_depths,
gt_quals,
variant_names,
het_names,
hom_alt_names,
hom_ref_names,
unknown_names,
info,
formatter=self.formatter)
if not all(
[predicate(gemini_row) for predicate in self.predicates]):
continue
if not self.for_browser:
return gemini_row
else:
return fields
def next(self):
"""
Return the GeminiRow object for the next query result.
"""
# we use a while loop since we may skip records based upon
# genotype filters. if we need to skip a record, we just
# throw a continue and keep trying. the alternative is to just
# recursively call self.next() if we need to skip, but this
# can quickly exceed the stack.
while (1):
try:
row = self.c.next()
except Exception as e:
self.conn.close()
raise StopIteration
gts = None
gt_types = None
gt_phases = None
gt_depths = None
gt_ref_depths = None
gt_alt_depths = None
gt_quals = None
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
if self._query_needs_genotype_info():
gts = compression.unpack_genotype_blob(row['gts'])
gt_types = \
compression.unpack_genotype_blob(row['gt_types'])
gt_phases = \
compression.unpack_genotype_blob(row['gt_phases'])
gt_depths = \
compression.unpack_genotype_blob(row['gt_depths'])
gt_ref_depths = \
compression.unpack_genotype_blob(row['gt_ref_depths'])
gt_alt_depths = \
compression.unpack_genotype_blob(row['gt_alt_depths'])
gt_quals = \
compression.unpack_genotype_blob(row['gt_quals'])
variant_samples = [x for x, y in enumerate(gt_types) if y == HET or
y == HOM_ALT]
variant_names = [self.idx_to_sample[x] for x in variant_samples]
het_samples = [x for x, y in enumerate(gt_types) if y == HET]
het_names = [self.idx_to_sample[x] for x in het_samples]
hom_alt_samples = [x for x, y in enumerate(gt_types) if y == HOM_ALT]
hom_alt_names = [self.idx_to_sample[x] for x in hom_alt_samples]
hom_ref_samples = [x for x, y in enumerate(gt_types) if y == HOM_REF]
hom_ref_names = [self.idx_to_sample[x] for x in hom_ref_samples]
unknown_samples = [x for x, y in enumerate(gt_types) if y == UNKNOWN]
unknown_names = [self.idx_to_sample[x] for x in unknown_samples]
families = map(str, list(set([self.idx_to_sample_object[x].family_id
for x in variant_samples])))
# skip the record if it does not meet the user's genotype filter
if self.gt_filter and not eval(self.gt_filter, locals()):
continue
fields = OrderedDict()
for idx, col in enumerate(self.report_cols):
if col == "*":
continue
if not col.startswith("gt") and not col.startswith("GT") and not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = self._info_dict_to_string(info)
else:
# reuse the original column name user requested
# e.g. replace gts[1085] with gts.NA20814
if '[' in col:
orig_col = self.gt_idx_to_name_map[col]
val = eval(col.strip())
if type(val) in [np.int8, np.int32, np.bool_]:
fields[orig_col] = int(val)
elif type(val) in [np.float32]:
fields[orig_col] = float(val)
else:
fields[orig_col] = val
else:
# asked for "gts" or "gt_types", e.g.
if col == "gts":
fields[col] = ','.join(gts)
elif col == "gt_types":
fields[col] = \
','.join(str(t) for t in gt_types)
elif col == "gt_phases":
fields[col] = \
','.join(str(p) for p in gt_phases)
elif col == "gt_depths":
fields[col] = \
','.join(str(d) for d in gt_depths)
elif col == "gt_quals":
fields[col] = \
','.join(str(d) for d in gt_quals)
elif col == "gt_ref_depths":
fields[col] = \
','.join(str(d) for d in gt_ref_depths)
elif col == "gt_alt_depths":
fields[col] = \
','.join(str(d) for d in gt_alt_depths)
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(variant_names)
fields["HET_samples"] = \
self.variant_samples_delim.join(het_names)
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(hom_alt_names)
if self.show_families:
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields, gts, gt_types, gt_phases,
gt_depths, gt_ref_depths, gt_alt_depths,
gt_quals, variant_names, het_names, hom_alt_names,
hom_ref_names, unknown_names, info,
formatter=self.formatter)
if not all([predicate(gemini_row) for predicate in self.predicates]):
continue
if not self.for_browser:
return gemini_row
else:
return fields
def row_2_GeminiRow(self, row):
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
fields = OrderedDict()
for col in self.report_cols:
if col == "*":
continue
if not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = _info_dict_to_string(info)
if self.show_variant_samples or self.needs_sample_names:
het_names = self._get_variant_samples(row['variant_id'], HET)
hom_alt_names = self._get_variant_samples(row['variant_id'],
HOM_ALT)
hom_ref_names = self._get_variant_samples(row['variant_id'],
HOM_REF)
unknown_names = self._get_variant_samples(row['variant_id'],
UNKNOWN)
variant_names = het_names | hom_alt_names
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(variant_names)
fields["HET_samples"] = \
self.variant_samples_delim.join(het_names)
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(hom_alt_names)
if self.show_families:
families = map(
str,
list(
set([
self.sample_to_sample_object[x].family_id
for x in variant_names
])))
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields,
variant_names,
het_names,
hom_alt_names,
hom_ref_names,
unknown_names,
info,
formatter=self.formatter)
if not all([predicate(gemini_row) for predicate in self.predicates]):
return None
if not self.for_browser:
return gemini_row
else:
return fields
def next(self):
"""
Return the GeminiRow object for the next query result.
"""
# we use a while loop since we may skip records based upon
# genotype filters. if we need to skip a record, we just
# throw a continue and keep trying. the alternative is to just
# recursively call self.next() if we need to skip, but this
# can quickly exceed the stack.
while (1):
try:
row = self.c.next()
except Exception as e:
self.conn.close()
raise StopIteration
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
unpacked = {'self': self}
unpack = compression.unpack_genotype_blob
if self._query_needs_genotype_info():
# TODO: see if HET, etc. are needed. if not, we can skip
# _group_samples_by_genotype
unpacked['gt_types'] = unpack(row['gt_types'])
genotype_dict = self._group_samples_by_genotype(unpacked['gt_types'])
if self.gt_filter or self.include_gt_cols:
for k in ('gts', 'gt_phases', 'gt_depths', 'gt_ref_depths',
'gt_alt_depths', 'gt_quals', 'gt_copy_numbers',
'gt_phred_ll_homref',
'gt_phred_ll_het',
'gt_phred_ll_homalt',
):
# only unpack what is needed.
if (self.gt_filter is not None and k in self.gt_filter) or self.include_gt_cols:
unpacked[k] = unpack(row[k])
# skip the record if it does not meet the user's genotype filter
# short circuit some expensive ops
try:
if self.gt_filter and not eval(self.gt_filter_compiled, unpacked):
continue
except TypeError: # tried to eval on a phred_ll column that was None
continue
het_names = genotype_dict[HET]
hom_alt_names = genotype_dict[HOM_ALT]
hom_ref_names = genotype_dict[HOM_REF]
unknown_names = genotype_dict[UNKNOWN]
variant_names = het_names + hom_alt_names
fields = OrderedDict()
for idx, col in enumerate(self.report_cols):
if col == "*":
continue
if not col[:2] in ("gt", "GT") and not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = self._info_dict_to_string(info)
else:
# reuse the original column name user requested
# e.g. replace gts[1085] with gts.NA20814
if '[' in col:
orig_col = self.gt_idx_to_name_map[col]
source, extra = col.split('[', 1)
if not source in unpacked:
unpacked[source] = unpack(row[source])
assert extra[-1] == ']'
if source.startswith('gt_phred_ll') and unpacked[source] is None:
fields[orig_col] = None
continue
idx = int(extra[:-1])
val = unpacked[source][idx]
#val = unpacked[col.split('[', 1)[0]]
if type(val) in (np.int8, np.int32, np.bool_):
fields[orig_col] = int(val)
elif type(val) in (np.float32,):
fields[orig_col] = float(val)
else:
fields[orig_col] = val
else:
# asked for "gts" or "gt_types", e.g.
if not col in unpacked:
unpacked[col] = unpack(row[col])
if unpacked[col] is not None:
fields[col] = ",".join(str(v) for v in unpacked[col])
else:
fields[col] = str(None)
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(self._filter_samples(variant_names))
fields["HET_samples"] = \
self.variant_samples_delim.join(self._filter_samples(genotype_dict[HET]))
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(self._filter_samples(genotype_dict[HOM_ALT]))
if self.show_families:
families = map(str, list(set([self.sample_to_sample_object[x].family_id
for x in variant_names])))
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields,
unpacked.get('gts'),
unpacked.get('gt_types'),
unpacked.get('gt_phases'),
unpacked.get('gt_depths'),
unpacked.get('gt_ref_depths'),
unpacked.get('gt_alt_depths'),
unpacked.get('gt_quals'),
unpacked.get('gt_copy_numbers'),
unpacked.get('gt_phred_ll_homref'),
unpacked.get('gt_phred_ll_het'),
unpacked.get('gt_phred_ll_homalt'),
variant_names,
het_names,
hom_alt_names,
hom_ref_names,
unknown_names,
info,
formatter=self.formatter)
if not all(predicate(gemini_row) for predicate in self.predicates):
continue
if not self.for_browser:
return gemini_row
else:
return fields
def next(self):
"""
Return the GeminiRow object for the next query result.
"""
# we use a while loop since we may skip records based upon
# genotype filters. if we need to skip a record, we just
# throw a continue and keep trying. the alternative is to just
# recursively call self.next() if we need to skip, but this
# can quickly exceed the stack.
while (1):
try:
row = self.c.next()
except Exception as e:
self.conn.close()
raise StopIteration
variant_names = []
het_names = []
hom_alt_names = []
hom_ref_names = []
unknown_names = []
info = None
if 'info' in self.report_cols:
info = compression.unpack_ordereddict_blob(row['info'])
unpacked = {'self': self}
unpack = compression.unpack_genotype_blob
if self._query_needs_genotype_info():
# TODO: see if HET, etc. are needed. if not, we can skip
# _group_samples_by_genotype
unpacked['gt_types'] = unpack(row['gt_types'])
genotype_dict = self._group_samples_by_genotype(
unpacked['gt_types'])
if self.gt_filter or self.include_gt_cols:
for k in ('gts', 'gt_phases', 'gt_depths', 'gt_ref_depths',
'gt_alt_depths', 'gt_quals', 'gt_copy_numbers'):
# only unpack what is needed.
if (self.gt_filter is not None and k
in self.gt_filter) or self.include_gt_cols:
unpacked[k] = unpack(row[k])
# skip the record if it does not meet the user's genotype filter
# short circuit some expensive ops
if self.gt_filter and not eval(self.gt_filter_compiled,
unpacked):
continue
het_names = genotype_dict[HET]
hom_alt_names = genotype_dict[HOM_ALT]
hom_ref_names = genotype_dict[HOM_REF]
unknown_names = genotype_dict[UNKNOWN]
variant_names = het_names + hom_alt_names
fields = OrderedDict()
for idx, col in enumerate(self.report_cols):
if col == "*":
continue
if not col[:2] in ("gt", "GT") and not col == "info":
fields[col] = row[col]
elif col == "info":
fields[col] = self._info_dict_to_string(info)
else:
# reuse the original column name user requested
# e.g. replace gts[1085] with gts.NA20814
if '[' in col:
orig_col = self.gt_idx_to_name_map[col]
source, extra = col.split('[', 1)
if not source in unpacked:
unpacked[source] = unpack(row[source])
assert extra[-1] == ']'
idx = int(extra[:-1])
val = unpacked[source][idx]
#val = unpacked[col.split('[', 1)[0]]
if type(val) in (np.int8, np.int32, np.bool_):
fields[orig_col] = int(val)
elif type(val) in (np.float32, ):
fields[orig_col] = float(val)
else:
fields[orig_col] = val
else:
# asked for "gts" or "gt_types", e.g.
if not col in unpacked:
unpacked[col] = unpack(row[col])
fields[col] = ",".join(str(v) for v in unpacked[col])
if self.show_variant_samples:
fields["variant_samples"] = \
self.variant_samples_delim.join(self._filter_samples(variant_names))
fields["HET_samples"] = \
self.variant_samples_delim.join(self._filter_samples(genotype_dict[HET]))
fields["HOM_ALT_samples"] = \
self.variant_samples_delim.join(self._filter_samples(genotype_dict[HOM_ALT]))
if self.show_families:
families = map(
str,
list(
set([
self.sample_to_sample_object[x].family_id
for x in variant_names
])))
fields["families"] = self.variant_samples_delim.join(families)
gemini_row = GeminiRow(fields,
unpacked.get('gts'),
unpacked.get('gt_types'),
unpacked.get('gt_phases'),
unpacked.get('gt_depths'),
unpacked.get('gt_ref_depths'),
unpacked.get('gt_alt_depths'),
unpacked.get('gt_quals'),
unpacked.get('gt_copy_numbers'),
variant_names,
het_names,
hom_alt_names,
hom_ref_names,
unknown_names,
info,
formatter=self.formatter)
if not all(predicate(gemini_row) for predicate in self.predicates):
continue
if not self.for_browser:
return gemini_row
else:
return fields