1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO base classes for HMMER-related code."""
from Bio._py3k import _as_bytes
from Bio.SearchIO._index import SearchIndexer
class _BaseHmmerTextIndexer(SearchIndexer):
"""Base indexer class for HMMER plain text output."""
def __init__(self, *args, **kwargs):
super(_BaseHmmerTextIndexer, self).__init__(*args, **kwargs)
self._preamble = _as_bytes('')
def get_raw(self, offset):
handle = self._handle
qresult_raw = _as_bytes('')
# read header first
if not self._preamble:
handle.seek(0)
while True:
line = handle.readline()
if line.startswith(self.qresult_start):
break
qresult_raw += line
else:
qresult_raw += self._preamble
# and read the qresult raw string
handle.seek(offset)
while True:
# preserve whitespace, don't use read_forward
line = handle.readline()
qresult_raw += line
# break when we've reached qresult end
if line.startswith(self.qresult_end) or not line:
break
return qresult_raw
|
