本文整理汇总了Python中Bio.SearchIO._model.QueryResult.blast_id方法的典型用法代码示例。如果您正苦于以下问题：Python QueryResult.blast_id方法的具体用法？Python QueryResult.blast_id怎么用？Python QueryResult.blast_id使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Bio.SearchIO._model.QueryResult的用法示例。
在下文中一共展示了QueryResult.blast_id方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: _parse_qresult
# 需要导入模块: from Bio.SearchIO._model import QueryResult [as 别名]
# 或者: from Bio.SearchIO._model.QueryResult import blast_id [as 别名]
def _parse_qresult(self):
"""Parse query results."""
# parse the queries
for event, qresult_elem in self.xml_iter:
# </Iteration> marks the end of a single query
# which means we can process it
if event == 'end' and qresult_elem.tag == 'Iteration':
# we'll use the following schema
# <!ELEMENT Iteration (
# Iteration_iter-num,
# Iteration_query-ID?,
# Iteration_query-def?,
# Iteration_query-len?,
# Iteration_hits?,
# Iteration_stat?,
# Iteration_message?)>
# assign query attributes with fallbacks
query_id = qresult_elem.findtext('Iteration_query-ID')
if query_id is None:
query_id = self._fallback['id']
query_desc = qresult_elem.findtext('Iteration_query-def')
if query_desc is None:
query_desc = self._fallback['description']
query_len = qresult_elem.findtext('Iteration_query-len')
if query_len is None:
query_len = self._fallback['len']
blast_query_id = query_id
# handle blast searches against databases with Blast's IDs
# 'Query_' marks the beginning of a BLAST+-generated ID,
# 'lcl|' marks the beginning of a BLAST legacy-generated ID
if not self._use_raw_query_ids and \
(query_id.startswith('Query_') or query_id.startswith('lcl|')):
# store the Blast-generated query ID
id_desc = query_desc.split(' ', 1)
query_id = id_desc[0]
try:
query_desc = id_desc[1]
except IndexError:
query_desc = ''
hit_list, key_list = [], []
for hit in self._parse_hit(qresult_elem.find('Iteration_hits'),
query_id):
if hit:
# need to keep track of hit IDs, since there could be duplicates,
if hit.id in key_list:
warnings.warn("Renaming hit ID %r to a BLAST-generated ID "
"%r since the ID was already matched "
"by your query %r. Your BLAST database may contain "
"duplicate entries." %
(hit.id, hit.blast_id, query_id), BiopythonParserWarning)
# fallback to Blast-generated IDs, if the ID is already present
# and restore the desc, too
hit.description = '%s %s' % (hit.id, hit.description)
hit.id = hit.blast_id
# and change the hit_id of the HSPs contained
for hsp in hit:
hsp.hit_id = hit.blast_id
else:
key_list.append(hit.id)
hit_list.append(hit)
# create qresult and assign its attributes
qresult = QueryResult(hit_list, query_id)
qresult.description = query_desc
qresult.seq_len = int(query_len)
qresult.blast_id = blast_query_id
for key, value in self._meta.items():
setattr(qresult, key, value)
# statistics are stored in Iteration_stat's 'grandchildren' with the
# following DTD
# <!ELEMENT Statistics (
# Statistics_db-num,
# Statistics_db-len,
# Statistics_hsp-len,
# Statistics_eff-space,
# Statistics_kappa,
# Statistics_lambda,
# Statistics_entropy)>
stat_iter_elem = qresult_elem.find('Iteration_stat')
if stat_iter_elem is not None:
stat_elem = stat_iter_elem.find('Statistics')
for key, val_info in _ELEM_QRESULT_OPT.items():
value = stat_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(qresult, val_info[0], value)
#.........这里部分代码省略.........