-
Notifications
You must be signed in to change notification settings - Fork 13
/
protein_sequence_helpers.py
60 lines (49 loc) · 1.88 KB
/
protein_sequence_helpers.py
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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
# Copyright (c) 2019. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Since multiple variant sequences can translate to the same amino acid sequence,
this module aggregates equivalent Translation objects into a single
ProteinSequence.
"""
from __future__ import print_function, division, absolute_import
from .common import groupby
from .logging import get_logger
from .protein_sequence import ProteinSequence
from .translation import Translation
logger = get_logger(__name__)
def sort_protein_sequences(protein_sequences):
"""
Sort protein sequences in decreasing order of priority
"""
return list(
sorted(
protein_sequences,
key=ProteinSequence.ascending_sort_key,
reverse=True))
def group_equivalent_translations(translations):
"""
Convert a list of Translation objects into a (potentially smaller) list
of ProteinSequence objects by grouping the equivalent amino acid sequences.
Parameters
----------
translations : list of Translation objects
Returns list of ProteinSequence objects
"""
protein_sequences = []
translation_groups = groupby(
translations,
key_fn=Translation.as_translation_key)
for equivalent_translations in translation_groups.values():
protein_sequences.append(ProteinSequence(equivalent_translations))
return protein_sequences