def _parse_hit(self, root_hit_elem, query_id):
"""Yield a generator object that transforms Iteration_hits XML elements into Hit objects (PRIVATE).
:param root_hit_elem: root element of the Iteration_hits tag.
:type root_hit_elem: XML element tag
:param query_id: QueryResult ID of this Hit
:type query_id: string
"""
# Hit level processing
# Hits are stored in the Iteration_hits tag, with the following
# DTD
# <!ELEMENT Hit (
# Hit_num,
# Hit_id,
# Hit_def,
# Hit_accession,
# Hit_len,
# Hit_hsps?)>
# feed the loop below an empty list so iteration still works
if root_hit_elem is None:
root_hit_elem = []
for hit_elem in root_hit_elem:
# BLAST sometimes mangles the sequence IDs and descriptions, so we need
# to extract the actual values.
raw_hit_id = hit_elem.findtext('Hit_id')
raw_hit_desc = hit_elem.findtext('Hit_def')
if not self._use_raw_hit_ids:
ids, descs, blast_hit_id = _extract_ids_and_descs(raw_hit_id, raw_hit_desc)
else:
ids, descs, blast_hit_id = [raw_hit_id], [raw_hit_desc], raw_hit_id
hit_id, alt_hit_ids = ids[0], ids[1:]
hit_desc, alt_hit_descs = descs[0], descs[1:]
hsps = [hsp for hsp in
self._parse_hsp(hit_elem.find('Hit_hsps'),
query_id, hit_id)]
hit = Hit(hsps)
hit.description = hit_desc
hit._id_alt = alt_hit_ids
hit._description_alt = alt_hit_descs
hit.blast_id = blast_hit_id
for key, val_info in _ELEM_HIT.items():
value = hit_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(hit, val_info[0], value)
# delete element after we finish parsing it
hit_elem.clear()
yield hit
def _parse_hit(self, root_hit_elem, query_id):
"""Generator that transforms Iteration_hits XML elements into Hit objects.
:param root_hit_elem: root element of the Iteration_hits tag.
:type root_hit_elem: XML element tag
:param query_id: QueryResult ID of this Hit
:type query_id: string
"""
# Hit level processing
# Hits are stored in the Iteration_hits tag, with the following
# DTD
# <!ELEMENT Hit (
# Hit_num,
# Hit_id,
# Hit_def,
# Hit_accession,
# Hit_len,
# Hit_hsps?)>
# feed the loop below an empty list so iteration still works
if root_hit_elem is None:
root_hit_elem = []
for hit_elem in root_hit_elem:
# create empty hit object
hit_id = hit_elem.findtext('Hit_id')
hit_desc = hit_elem.findtext('Hit_def')
# handle blast searches against databases with Blast's IDs
if hit_id.startswith('gnl|BL_ORD_ID|'):
blast_hit_id = hit_id
id_desc = hit_desc.split(' ', 1)
hit_id = id_desc[0]
try:
hit_desc = id_desc[1]
except IndexError:
hit_desc = ''
else:
blast_hit_id = ''
# combine primary ID and defline first before splitting
full_id_desc = hit_id + ' ' + hit_desc
id_descs = [(x.strip(), y.strip()) for x, y in \
[a.split(' ', 1) for a in full_id_desc.split(' >')]]
hit_id, hit_desc = id_descs[0]
hsps = [hsp for hsp in
self._parse_hsp(hit_elem.find('Hit_hsps'),
query_id, hit_id)]
hit = Hit(hsps)
hit.description = hit_desc
hit._id_alt = [x[0] for x in id_descs[1:]]
hit._description_alt = [x[1] for x in id_descs[1:]]
# blast_hit_id is only set if the hit ID is Blast-generated
hit._blast_id = blast_hit_id
for key, val_info in _ELEM_HIT.items():
value = hit_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(hit, val_info[0], value)
# delete element after we finish parsing it
hit_elem.clear()
yield hit
def _parse_hit(self, root_hit_elem, query_id):
"""Generator that transforms Iteration_hits XML elements into Hit objects.
:param root_hit_elem: root element of the Iteration_hits tag.
:type root_hit_elem: XML element tag
:param query_id: QueryResult ID of this Hit
:type query_id: string
"""
# Hit level processing
# Hits are stored in the Iteration_hits tag, with the following
# DTD
# <!ELEMENT Hit (
# Hit_num,
# Hit_id,
# Hit_def,
# Hit_accession,
# Hit_len,
# Hit_hsps?)>
# feed the loop below an empty list so iteration still works
if root_hit_elem is None:
root_hit_elem = []
for hit_elem in root_hit_elem:
# create empty hit object
hit_id = hit_elem.findtext('Hit_id')
hit_desc = hit_elem.findtext('Hit_def')
# handle blast searches against databases with Blast's IDs
if hit_id.startswith('gnl|BL_ORD_ID|'):
blast_hit_id = hit_id
id_desc = hit_desc.split(' ', 1)
hit_id = id_desc[0]
try:
hit_desc = id_desc[1]
except IndexError:
hit_desc = ''
else:
blast_hit_id = ''
# combine primary ID and defline first before splitting
full_id_desc = hit_id + ' ' + hit_desc
id_descs = _extract_ids_and_descs(full_id_desc)
hit_id, hit_desc = id_descs[0]
hsps = [
hsp for hsp in self._parse_hsp(hit_elem.find('Hit_hsps'),
query_id, hit_id)
]
hit = Hit(hsps)
hit.description = hit_desc
hit._id_alt = [x[0] for x in id_descs[1:]]
hit._description_alt = [x[1] for x in id_descs[1:]]
# blast_hit_id is only set if the hit ID is Blast-generated
hit._blast_id = blast_hit_id
for key, val_info in _ELEM_HIT.items():
value = hit_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(hit, val_info[0], value)
# delete element after we finish parsing it
hit_elem.clear()
yield hit
def _parse_hit(self, root_hit_elem, query_id):
"""Yield a generator object that transforms Iteration_hits XML elements into Hit objects (PRIVATE).
:param root_hit_elem: root element of the Iteration_hits tag.
:type root_hit_elem: XML element tag
:param query_id: QueryResult ID of this Hit
:type query_id: string
"""
# Hit level processing
# Hits are stored in the Iteration_hits tag, with the following
# DTD
# <!ELEMENT Hit (
# Hit_num,
# Hit_id,
# Hit_def,
# Hit_accession,
# Hit_len,
# Hit_hsps?)>
# feed the loop below an empty list so iteration still works
if root_hit_elem is None:
root_hit_elem = []
for hit_elem in root_hit_elem:
# BLAST sometimes mangles the sequence IDs and descriptions, so we need
# to extract the actual values.
raw_hit_id = hit_elem.findtext('Hit_id')
raw_hit_desc = hit_elem.findtext('Hit_def')
if not self._use_raw_hit_ids:
ids, descs, blast_hit_id = _extract_ids_and_descs(
raw_hit_id, raw_hit_desc)
else:
ids, descs, blast_hit_id = [raw_hit_id], [raw_hit_desc
], raw_hit_id
hit_id, alt_hit_ids = ids[0], ids[1:]
hit_desc, alt_hit_descs = descs[0], descs[1:]
hsps = [
hsp for hsp in self._parse_hsp(hit_elem.find('Hit_hsps'),
query_id, hit_id)
]
hit = Hit(hsps)
hit.description = hit_desc
hit._id_alt = alt_hit_ids
hit._description_alt = alt_hit_descs
hit.blast_id = blast_hit_id
for key, val_info in _ELEM_HIT.items():
value = hit_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(hit, val_info[0], value)
# delete element after we finish parsing it
hit_elem.clear()
yield hit
