Mercurial > repos > fubar > jbrowse2dev

comparison jbrowse2/gff3_rebase.py @ 0:cd5d63cd0eb5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 03 Jan 2024 01:36:39 +0000
parents
children 88b9b105c09b
comparison
equal deleted inserted replaced
-1:000000000000 0:cd5d63cd0eb5
1 #!/usr/bin/env python
2 import argparse
3 import copy
4 import logging
5 import sys
6
7 from BCBio import GFF
8 from Bio.SeqFeature import FeatureLocation
9
10 logging.basicConfig(level=logging.INFO)
11 log = logging.getLogger(__name__)
12
13 __author__ = "Eric Rasche"
14 __version__ = "0.4.0"
15 __maintainer__ = "Eric Rasche"
16 __email__ = "esr@tamu.edu"
17
18
19 def feature_lambda(feature_list, test, test_kwargs, subfeatures=True):
20 """Recursively search through features, testing each with a test function, yielding matches.
21
22 GFF3 is a hierachical data structure, so we need to be able to recursively
23 search through features. E.g. if you're looking for a feature with
24 ID='bob.42', you can't just do a simple list comprehension with a test
25 case. You don't know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.
26
27 :type feature_list: list
28 :param feature_list: an iterable of features
29
30 :type test: function reference
31 :param test: a closure with the method signature (feature, **kwargs) where
32 the kwargs are those passed in the next argument. This
33 function should return True or False, True if the feature is
34 to be yielded as part of the main feature_lambda function, or
35 False if it is to be ignored. This function CAN mutate the
36 features passed to it (think "apply").
37
38 :type test_kwargs: dictionary
39 :param test_kwargs: kwargs to pass to your closure when it is called.
40
41 :type subfeatures: boolean
42 :param subfeatures: when a feature is matched, should just that feature be
43 yielded to the caller, or should the entire sub_feature
44 tree for that feature be included? subfeatures=True is
45 useful in cases such as searching for a gene feature,
46 and wanting to know what RBS/Shine_Dalgarno_sequences
47 are in the sub_feature tree (which can be accomplished
48 with two feature_lambda calls). subfeatures=False is
49 useful in cases when you want to process (and possibly
50 return) the entire feature tree, such as applying a
51 qualifier to every single feature.
52
53 :rtype: yielded list
54 :return: Yields a list of matching features.
55 """
56 # Either the top level set of [features] or the subfeature attribute
57 for feature in feature_list:
58 if test(feature, **test_kwargs):
59 if not subfeatures:
60 feature_copy = copy.deepcopy(feature)
61 feature_copy.sub_features = []
62 yield feature_copy
63 else:
64 yield feature
65
66 if hasattr(feature, 'sub_features'):
67 for x in feature_lambda(feature.sub_features, test, test_kwargs, subfeatures=subfeatures):
68 yield x
69
70
71 def feature_test_qual_value(feature, **kwargs):
72 """Test qualifier values.
73
74 For every feature, check that at least one value in
75 feature.quailfiers(kwargs['qualifier']) is in kwargs['attribute_list']
76 """
77 for attribute_value in feature.qualifiers.get(kwargs['qualifier'], []):
78 if attribute_value in kwargs['attribute_list']:
79 return True
80 return False
81
82
83 def __get_features(child, interpro=False):
84 child_features = {}
85 for rec in GFF.parse(child):
86 # Only top level
87 for feature in rec.features:
88 # Get the record id as parent_feature_id (since this is how it will be during remapping)
89 parent_feature_id = rec.id
90 # If it's an interpro specific gff3 file
91 if interpro:
92 # Then we ignore polypeptide features as they're useless
93 if feature.type == 'polypeptide':
94 continue
95 # If there's an underscore, we strip up to that underscore?
96 # I do not know the rationale for this, removing.
97 # if '_' in parent_feature_id:
98 # parent_feature_id = parent_feature_id[parent_feature_id.index('_') + 1:]
99
100 try:
101 child_features[parent_feature_id].append(feature)
102 except KeyError:
103 child_features[parent_feature_id] = [feature]
104 # Keep a list of feature objects keyed by parent record id
105 return child_features
106
107
108 def __update_feature_location(feature, parent, protein2dna):
109 start = feature.location.start
110 end = feature.location.end
111 if protein2dna:
112 start *= 3
113 end *= 3
114
115 if parent.location.strand >= 0:
116 ns = parent.location.start + start
117 ne = parent.location.start + end
118 st = +1
119 else:
120 ns = parent.location.end - end
121 ne = parent.location.end - start
122 st = -1
123
124 # Don't let start/stops be less than zero. It's technically valid for them
125 # to be (at least in the model I'm working with) but it causes numerous
126 # issues.
127 #
128 # Instead, we'll replace with %3 to try and keep it in the same reading
129 # frame that it should be in.
130 if ns < 0:
131 ns %= 3
132 if ne < 0:
133 ne %= 3
134
135 feature.location = FeatureLocation(ns, ne, strand=st)
136
137 if hasattr(feature, 'sub_features'):
138 for subfeature in feature.sub_features:
139 __update_feature_location(subfeature, parent, protein2dna)
140
141
142 def rebase(parent, child, interpro=False, protein2dna=False, map_by='ID'):
143 # get all of the features we will be re-mapping in a dictionary, keyed by parent feature ID
144 child_features = __get_features(child, interpro=interpro)
145
146 for rec in GFF.parse(parent):
147 replacement_features = []
148 for feature in feature_lambda(
149 rec.features,
150 # Filter features in the parent genome by those that are
151 # "interesting", i.e. have results in child_features array.
152 # Probably an unnecessary optimisation.
153 feature_test_qual_value,
154 {
155 'qualifier': map_by,
156 'attribute_list': child_features.keys(),
157 },
158 subfeatures=False):
159
160 # Features which will be re-mapped
161 to_remap = child_features[feature.id]
162 # TODO: update starts
163 fixed_features = []
164 for x in to_remap:
165 # Then update the location of the actual feature
166 __update_feature_location(x, feature, protein2dna)
167
168 if interpro:
169 for y in ('status', 'Target'):
170 try:
171 del x.qualifiers[y]
172 except Exception:
173 pass
174
175 fixed_features.append(x)
176 replacement_features.extend(fixed_features)
177 # We do this so we don't include the original set of features that we
178 # were rebasing against in our result.
179 rec.features = replacement_features
180 rec.annotations = {}
181 GFF.write([rec], sys.stdout)
182
183
184 if __name__ == '__main__':
185 parser = argparse.ArgumentParser(description='rebase gff3 features against parent locations', epilog="")
186 parser.add_argument('parent', type=argparse.FileType('r'), help='Parent GFF3 annotations')
187 parser.add_argument('child', type=argparse.FileType('r'), help='Child GFF3 annotations to rebase against parent')
188 parser.add_argument('--interpro', action='store_true',
189 help='Interpro specific modifications')
190 parser.add_argument('--protein2dna', action='store_true',
191 help='Map protein translated results to original DNA data')
192 parser.add_argument('--map_by', help='Map by key', default='ID')
193 args = parser.parse_args()
194 rebase(**vars(args))