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
|
# Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO base classes for Infernal-related code."""
from Bio.SearchIO._model import Hit
class _BaseInfernalParser:
"""Abstract class for Infernal parser objects."""
def _add_hit_to_dict(self, hit_attrs, hsp, hit_dict):
"""Add a hit information to the hit container (PRIVATE)."""
# add the hit to the container dict, creating a new
# entry if it does not exist yet
hid = hit_attrs["id"]
if hid not in hit_dict:
hit_dict[hid] = {"attrs": hit_attrs, "hsps": []}
else:
assert hit_dict[hid]["attrs"]["query_id"] == hit_attrs["query_id"]
assert hit_dict[hid]["attrs"]["description"] == hit_attrs["description"]
hit_dict[hid]["hsps"].append(hsp)
def _hit_to_list(self, hit_dict):
"""Create a Hit list from the hit container (PRIVATE)."""
hit_list = []
for hit_info in hit_dict.values():
hit = Hit(hit_info["hsps"])
for attr, value in hit_info["attrs"].items():
setattr(hit, attr, value)
hit_list.append(hit)
return hit_list
|
