本文整理汇总了Python中Bio.SearchIO._model.HSP.env_start方法的典型用法代码示例。如果您正苦于以下问题：Python HSP.env_start方法的具体用法？Python HSP.env_start怎么用？Python HSP.env_start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.HSP的用法示例。
在下文中一共展示了HSP.env_start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: _create_hits
# 需要导入模块: from Bio.SearchIO._model import HSP [as 别名]
# 或者: from Bio.SearchIO._model.HSP import env_start [as 别名]
def _create_hits(self, hit_attrs, qid, qdesc):
"""Parses a HMMER3 hsp block, beginning with the hsp table."""
# read through until the beginning of the hsp block
self._read_until(lambda line: line.startswith('Internal pipeline')
or line.startswith('>>'))
# start parsing the hsp block
hit_list = []
while True:
if self.line.startswith('Internal pipeline'):
# by this time we should've emptied the hit attr list
assert len(hit_attrs) == 0
return hit_list
assert self.line.startswith('>>')
hid, hdesc = self.line[len('>> '):].split(' ', 1)
hdesc = hdesc.strip()
# read through the hsp table header and move one more line
self._read_until(lambda line:
line.startswith(' --- ------ ----- --------') or
line.startswith(' [No individual domains'))
self.line = read_forward(self.handle)
# parse the hsp table for the current hit
hsp_list = []
while True:
# break out of hsp parsing if there are no hits, it's the last hsp
# or it's the start of a new hit
if self.line.startswith(' [No targets detected that satisfy') or \
self.line.startswith(' [No individual domains') or \
self.line.startswith('Internal pipeline statistics summary:') or \
self.line.startswith(' Alignments for each domain:') or \
self.line.startswith('>>'):
hit_attr = hit_attrs.pop(0)
hit = Hit(hsp_list)
for attr, value in hit_attr.items():
if attr == "description":
cur_val = getattr(hit, attr)
if cur_val and value and cur_val.startswith(value):
continue
setattr(hit, attr, value)
if not hit:
hit.query_description = qdesc
hit_list.append(hit)
break
parsed = [x for x in self.line.strip().split(' ') if x]
assert len(parsed) == 16
# parsed column order:
# index, is_included, bitscore, bias, evalue_cond, evalue
# hmmfrom, hmmto, query_ends, hit_ends, alifrom, alito,
# envfrom, envto, acc_avg
frag = HSPFragment(hid, qid)
# set query and hit descriptions if they are defined / nonempty string
if qdesc:
frag.query_description = qdesc
if hdesc:
frag.hit_description = hdesc
# HMMER3 alphabets are always protein alphabets
frag.alphabet = generic_protein
# depending on whether the program is hmmsearch, hmmscan, or phmmer
# {hmm,ali}{from,to} can either be hit_{from,to} or query_{from,to}
# for hmmscan, hit is the hmm profile, query is the sequence
if self._meta.get('program') == 'hmmscan':
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[6]) - 1
frag.hit_end = int(parsed[7])
frag.query_start = int(parsed[9]) - 1
frag.query_end = int(parsed[10])
elif self._meta.get('program') in ['hmmsearch', 'phmmer']:
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[9]) - 1
frag.hit_end = int(parsed[10])
frag.query_start = int(parsed[6]) - 1
frag.query_end = int(parsed[7])
# strand is always 0, since HMMER now only handles protein
frag.hit_strand = frag.query_strand = 0
hsp = HSP([frag])
hsp.domain_index = int(parsed[0])
hsp.is_included = parsed[1] == '!'
hsp.bitscore = float(parsed[2])
hsp.bias = float(parsed[3])
hsp.evalue_cond = float(parsed[4])
hsp.evalue = float(parsed[5])
if self._meta.get('program') == 'hmmscan':
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[8]
hsp.query_endtype = parsed[11]
elif self._meta.get('program') in ['hmmsearch', 'phmmer']:
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[11]
hsp.query_endtype = parsed[8]
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.env_start = int(parsed[12]) - 1
hsp.env_end = int(parsed[13])
hsp.env_endtype = parsed[14]
hsp.acc_avg = float(parsed[15])
#.........这里部分代码省略.........