|
1
|
|
|
# Copyright (C) 2010-2018 by Haibao Tang et al. All rights reserved. |
|
2
|
|
|
# |
|
3
|
|
|
# This code is part of the goatools distribution and goverend by its |
|
4
|
|
|
# license. Please see the LICENSE file included with goatools. |
|
5
|
|
|
|
|
6
|
|
|
|
|
7
|
|
|
"""Read and store Gene Ontology's obo file.""" |
|
8
|
|
|
# -*- coding: UTF-8 -*- |
|
9
|
|
|
from __future__ import print_function |
|
10
|
|
|
|
|
11
|
|
|
import sys |
|
12
|
|
|
import os |
|
13
|
|
|
from goatools.godag.obo_optional_attributes import OboOptionalAttrs |
|
14
|
|
|
from goatools.godag.typedef import TypeDef |
|
15
|
|
|
from goatools.godag.typedef import add_to_typedef |
|
16
|
|
|
|
|
17
|
|
|
GraphEngines = ("pygraphviz", "pydot") |
|
18
|
|
|
|
|
19
|
|
|
__copyright__ = "Copyright (C) 2010-2018, H Tang et al., All rights reserved." |
|
20
|
|
|
__author__ = "various" |
|
21
|
|
|
|
|
22
|
|
|
|
|
23
|
|
|
#pylint: disable=too-few-public-methods |
|
24
|
|
|
class OBOReader(object): |
|
25
|
|
|
"""Read goatools.org's obo file. Load into this iterable class. |
|
26
|
|
|
|
|
27
|
|
|
Download obo from: http://geneontology.org/ontology/go-basic.obo |
|
28
|
|
|
|
|
29
|
|
|
>>> reader = OBOReader() |
|
30
|
|
|
>>> for rec in reader: |
|
31
|
|
|
print(rec) |
|
32
|
|
|
""" |
|
33
|
|
|
|
|
34
|
|
|
# Scalar attributes for Typedefs: |
|
35
|
|
|
# 'is_class_level', 'is_metadata_tag', |
|
36
|
|
|
# 'is_transitive', 'transitive_over']) |
|
37
|
|
|
|
|
38
|
|
|
def __init__(self, obo_file="go-basic.obo", optional_attrs=None): |
|
39
|
|
|
"""Read obo file. Load dictionary.""" |
|
40
|
|
|
self.optobj = self._init_optional_attrs(optional_attrs) # OboOptionalAttrs or None |
|
41
|
|
|
self.format_version = None # e.g., "1.2" of "format-version:" line |
|
42
|
|
|
self.data_version = None # e.g., "releases/2016-07-07" from "data-version:" line |
|
43
|
|
|
self.typedefs = {} |
|
44
|
|
|
|
|
45
|
|
|
# True if obo file exists or if a link to an obo file exists. |
|
46
|
|
|
if os.path.isfile(obo_file): |
|
47
|
|
|
self.obo_file = obo_file |
|
48
|
|
|
# GOTerm attributes that are necessary for any operations: |
|
49
|
|
|
else: |
|
50
|
|
|
raise Exception("COULD NOT READ({OBO})\n" |
|
51
|
|
|
"download obo file first\n " |
|
52
|
|
|
"[http://geneontology.org/ontology/" |
|
53
|
|
|
"go-basic.obo]".format(OBO=obo_file)) |
|
54
|
|
|
|
|
55
|
|
|
def __iter__(self): |
|
56
|
|
|
"""Return one GO Term record at a time from an obo file.""" |
|
57
|
|
|
# Wait to open file until needed. Automatically close file when done. |
|
58
|
|
|
with open(self.obo_file) as fstream: |
|
59
|
|
|
rec_curr = None # Stores current GO Term |
|
60
|
|
|
typedef_curr = None # Stores current typedef |
|
61
|
|
|
for line in fstream: |
|
62
|
|
|
# obo lines start with any of: [Term], [Typedef], /^\S+:/, or /^\s*/ |
|
63
|
|
|
if self.data_version is None: |
|
64
|
|
|
self._init_obo_version(line) |
|
65
|
|
|
if rec_curr is None and line[0:6].lower() == "[term]": |
|
66
|
|
|
rec_curr = GOTerm() |
|
67
|
|
|
if self.optobj: |
|
68
|
|
|
self.optobj.init_datamembers(rec_curr) |
|
69
|
|
|
elif typedef_curr is None and line[0:9].lower() == "[typedef]": |
|
70
|
|
|
typedef_curr = TypeDef() |
|
71
|
|
|
elif rec_curr is not None or typedef_curr is not None: |
|
72
|
|
|
line = line.rstrip() # chomp |
|
73
|
|
|
if line: |
|
74
|
|
|
self._add_to_obj(rec_curr, typedef_curr, line) |
|
75
|
|
|
else: |
|
76
|
|
|
if rec_curr is not None: |
|
77
|
|
|
yield rec_curr |
|
78
|
|
|
rec_curr = None |
|
79
|
|
|
elif typedef_curr is not None: |
|
80
|
|
|
# Save typedef. |
|
81
|
|
|
self.typedefs[typedef_curr.id] = typedef_curr |
|
82
|
|
|
typedef_curr = None |
|
83
|
|
|
# Return last record, if necessary |
|
84
|
|
|
if rec_curr is not None: |
|
85
|
|
|
yield rec_curr |
|
86
|
|
|
|
|
87
|
|
|
def _add_to_obj(self, rec_curr, typedef_curr, line): |
|
88
|
|
|
"""Add information on line to GOTerm or Typedef.""" |
|
89
|
|
|
if rec_curr is not None: |
|
90
|
|
|
self._add_to_ref(rec_curr, line) |
|
91
|
|
|
else: |
|
92
|
|
|
add_to_typedef(typedef_curr, line) |
|
93
|
|
|
|
|
94
|
|
|
def _init_obo_version(self, line): |
|
95
|
|
|
"""Save obo version and release.""" |
|
96
|
|
|
if line[0:14] == "format-version": |
|
97
|
|
|
self.format_version = line[16:-1] |
|
98
|
|
|
if line[0:12] == "data-version": |
|
99
|
|
|
self.data_version = line[14:-1] |
|
100
|
|
|
|
|
101
|
|
|
def _add_to_ref(self, rec_curr, line): |
|
102
|
|
|
"""Add new fields to the current reference.""" |
|
103
|
|
|
# Examples of record lines containing ':' include: |
|
104
|
|
|
# id: GO:0000002 |
|
105
|
|
|
# name: mitochondrial genome maintenance |
|
106
|
|
|
# namespace: biological_process |
|
107
|
|
|
# def: "The maintenance of ... |
|
108
|
|
|
# is_a: GO:0007005 ! mitochondrion organization |
|
109
|
|
|
if line[:4] == "id: ": |
|
110
|
|
|
assert not rec_curr.id |
|
111
|
|
|
rec_curr.id = line[4:] |
|
112
|
|
|
elif line[:8] == "alt_id: ": |
|
113
|
|
|
rec_curr.alt_ids.add(line[8:]) |
|
114
|
|
|
elif line[:6] == "name: ": |
|
115
|
|
|
assert not rec_curr.name |
|
116
|
|
|
rec_curr.name = line[6:] |
|
117
|
|
|
elif line[:11] == "namespace: ": |
|
118
|
|
|
assert not rec_curr.namespace |
|
119
|
|
|
rec_curr.namespace = line[11:] |
|
120
|
|
|
elif line[:6] == "is_a: ": |
|
121
|
|
|
rec_curr._parents.add(line[6:].split()[0]) |
|
122
|
|
|
elif line[:13] == "is_obsolete: " and line[13:] == "true": |
|
123
|
|
|
rec_curr.is_obsolete = True |
|
124
|
|
|
elif self.optobj and ':' in line: |
|
125
|
|
|
self.optobj.update_rec(rec_curr, line) |
|
126
|
|
|
|
|
127
|
|
|
@staticmethod |
|
128
|
|
|
def _init_optional_attrs(optional_attrs): |
|
129
|
|
|
"""Create OboOptionalAttrs or return None.""" |
|
130
|
|
|
if optional_attrs is None: |
|
131
|
|
|
return None |
|
132
|
|
|
opts = OboOptionalAttrs.get_optional_attrs(optional_attrs) |
|
133
|
|
|
if opts: |
|
134
|
|
|
return OboOptionalAttrs(opts) |
|
135
|
|
|
|
|
136
|
|
|
|
|
137
|
|
|
class GOTerm(object): |
|
138
|
|
|
""" |
|
139
|
|
|
GO term, actually contain a lot more properties than interfaced here |
|
140
|
|
|
""" |
|
141
|
|
|
|
|
142
|
|
|
def __init__(self): |
|
143
|
|
|
self.id = "" # GO:NNNNNNN |
|
144
|
|
|
self.name = "" # description |
|
145
|
|
|
self.namespace = "" # BP, CC, MF |
|
146
|
|
|
self._parents = set() # is_a basestring of parents |
|
147
|
|
|
self.parents = set() # parent records |
|
148
|
|
|
self.children = set() # children records |
|
149
|
|
|
self.level = None # shortest distance from root node |
|
150
|
|
|
self.depth = None # longest distance from root node |
|
151
|
|
|
self.is_obsolete = False # is_obsolete |
|
152
|
|
|
self.alt_ids = set() # alternative identifiers |
|
153
|
|
|
|
|
154
|
|
|
def __str__(self): |
|
155
|
|
|
ret = ['{GO}\t'.format(GO=self.id)] |
|
156
|
|
|
if self.level is not None: |
|
157
|
|
|
ret.append('level-{L:>02}\t'.format(L=self.level)) |
|
158
|
|
|
if self.depth is not None: |
|
159
|
|
|
ret.append('depth-{D:>02}\t'.format(D=self.depth)) |
|
160
|
|
|
ret.append('{NAME} [{NS}]'.format(NAME=self.name, NS=self.namespace)) |
|
161
|
|
|
if self.is_obsolete: |
|
162
|
|
|
ret.append('obsolete') |
|
163
|
|
|
return ''.join(ret) |
|
164
|
|
|
|
|
165
|
|
|
def __repr__(self): |
|
166
|
|
|
"""Print GO id and all attributes in GOTerm class.""" |
|
167
|
|
|
ret = ["GOTerm('{ID}'):".format(ID=self.id)] |
|
168
|
|
|
for key, val in self.__dict__.items(): |
|
169
|
|
|
if isinstance(val, int) or isinstance(val, str): |
|
170
|
|
|
ret.append("{K}:{V}".format(K=key, V=val)) |
|
171
|
|
|
elif val is not None: |
|
172
|
|
|
ret.append("{K}: {V} items".format(K=key, V=len(val))) |
|
173
|
|
|
if len(val) < 10: |
|
174
|
|
|
if not isinstance(val, dict): |
|
175
|
|
|
for elem in val: |
|
176
|
|
|
ret.append(" {ELEM}".format(ELEM=elem)) |
|
177
|
|
|
else: |
|
178
|
|
|
for (typedef, terms) in val.items(): |
|
179
|
|
|
ret.append(" {TYPEDEF}: {NTERMS} items" |
|
180
|
|
|
.format(TYPEDEF=typedef, |
|
181
|
|
|
NTERMS=len(terms))) |
|
182
|
|
|
for term in terms: |
|
183
|
|
|
ret.append(" {TERM}".format(TERM=term)) |
|
184
|
|
|
else: |
|
185
|
|
|
ret.append("{K}: None".format(K=key)) |
|
186
|
|
|
return "\n ".join(ret) |
|
187
|
|
|
|
|
188
|
|
|
def has_parent(self, term): |
|
189
|
|
|
"""Return True if this GO object has a parent GO ID.""" |
|
190
|
|
|
for parent in self.parents: |
|
191
|
|
|
if parent.id == term or parent.has_parent(term): |
|
192
|
|
|
return True |
|
193
|
|
|
return False |
|
194
|
|
|
|
|
195
|
|
|
def has_child(self, term): |
|
196
|
|
|
"""Return True if this GO object has a child GO ID.""" |
|
197
|
|
|
for parent in self.children: |
|
198
|
|
|
if parent.id == term or parent.has_child(term): |
|
199
|
|
|
return True |
|
200
|
|
|
return False |
|
201
|
|
|
|
|
202
|
|
|
def get_all_parents(self): |
|
203
|
|
|
"""Return all parent GO IDs.""" |
|
204
|
|
|
all_parents = set() |
|
205
|
|
|
for parent in self.parents: |
|
206
|
|
|
all_parents.add(parent.id) |
|
207
|
|
|
all_parents |= parent.get_all_parents() |
|
208
|
|
|
return all_parents |
|
209
|
|
|
|
|
210
|
|
|
def get_all_upper(self): |
|
211
|
|
|
"""Return all parent GO IDs through both 'is_a' and all relationships.""" |
|
212
|
|
|
all_upper = set() |
|
213
|
|
|
for upper in self.get_goterms_upper(): |
|
214
|
|
|
all_upper.add(upper.id) |
|
215
|
|
|
all_upper |= upper.get_all_upper() |
|
216
|
|
|
return all_upper |
|
217
|
|
|
|
|
218
|
|
|
def get_all_children(self): |
|
219
|
|
|
"""Return all children GO IDs.""" |
|
220
|
|
|
all_children = set() |
|
221
|
|
|
for parent in self.children: |
|
222
|
|
|
all_children.add(parent.id) |
|
223
|
|
|
all_children |= parent.get_all_children() |
|
224
|
|
|
return all_children |
|
225
|
|
|
|
|
226
|
|
|
def get_all_lower(self): |
|
227
|
|
|
"""Return all parent GO IDs through both reverse 'is_a' and all relationships.""" |
|
228
|
|
|
all_lower = set() |
|
229
|
|
|
for lower in self.get_goterms_lower(): |
|
230
|
|
|
all_lower.add(lower.id) |
|
231
|
|
|
all_lower |= lower.get_all_lower() |
|
232
|
|
|
return all_lower |
|
233
|
|
|
|
|
234
|
|
|
def get_all_parent_edges(self): |
|
235
|
|
|
"""Return tuples for all parent GO IDs, containing current GO ID and parent GO ID.""" |
|
236
|
|
|
all_parent_edges = set() |
|
237
|
|
|
for parent in self.parents: |
|
238
|
|
|
all_parent_edges.add((self.id, parent.id)) |
|
239
|
|
|
all_parent_edges |= parent.get_all_parent_edges() |
|
240
|
|
|
return all_parent_edges |
|
241
|
|
|
|
|
242
|
|
|
def get_all_child_edges(self): |
|
243
|
|
|
"""Return tuples for all child GO IDs, containing current GO ID and child GO ID.""" |
|
244
|
|
|
all_child_edges = set() |
|
245
|
|
|
for parent in self.children: |
|
246
|
|
|
all_child_edges.add((parent.id, self.id)) |
|
247
|
|
|
all_child_edges |= parent.get_all_child_edges() |
|
248
|
|
|
return all_child_edges |
|
249
|
|
|
|
|
250
|
|
|
def get_goterms_upper(self): |
|
251
|
|
|
"""Returns a set containing parents and relationship GO Terms.""" |
|
252
|
|
|
# Requires GODag is created with 'relationship' in optional_attrs argument |
|
253
|
|
|
# pylint: disable=no-member |
|
254
|
|
|
return set.union(self.parents, *self.relationship.values()) |
|
255
|
|
|
|
|
256
|
|
|
def get_goterms_lower(self): |
|
257
|
|
|
"""Returns a set containing children and reverse-relationship GO Terms.""" |
|
258
|
|
|
# Requires GODag is created with 'relationship' in optional_attrs argument |
|
259
|
|
|
# pylint: disable=no-member |
|
260
|
|
|
return set.union(self.children, *self.relationship_rev.values()) |
|
261
|
|
|
|
|
262
|
|
|
|
|
263
|
|
|
#### def write_hier_rec(self, gos_printed, out=sys.stdout, |
|
264
|
|
|
#### len_dash=1, max_depth=None, num_child=None, short_prt=False, |
|
265
|
|
|
#### include_only=None, go_marks=None, |
|
266
|
|
|
#### depth=1, depth_dashes="-"): |
|
267
|
|
|
#### """Write hierarchy for a GO Term record.""" |
|
268
|
|
|
#### # Added by DV Klopfenstein |
|
269
|
|
|
#### goid = self.id |
|
270
|
|
|
#### # Shortens hierarchy report by only printing the hierarchy |
|
271
|
|
|
#### # for the sub-set of user-specified GO terms which are connected. |
|
272
|
|
|
#### if include_only is not None and goid not in include_only: |
|
273
|
|
|
#### return |
|
274
|
|
|
#### nrp = short_prt and goid in gos_printed |
|
275
|
|
|
#### if go_marks is not None: |
|
276
|
|
|
#### out.write('{} '.format('>' if goid in go_marks else ' ')) |
|
277
|
|
|
#### if len_dash is not None: |
|
278
|
|
|
#### # Default character indicating hierarchy level is '-'. |
|
279
|
|
|
#### # '=' is used to indicate a hierarchical path printed in detail previously. |
|
280
|
|
|
#### letter = '-' if not nrp or not self.children else '=' |
|
281
|
|
|
#### depth_dashes = ''.join([letter]*depth) |
|
282
|
|
|
#### out.write('{DASHES:{N}} '.format(DASHES=depth_dashes, N=len_dash)) |
|
283
|
|
|
#### if num_child is not None: |
|
284
|
|
|
#### out.write('{N:>5} '.format(N=len(self.get_all_children()))) |
|
285
|
|
|
#### out.write('{GO}\tL-{L:>02}\tD-{D:>02}\t{desc}\n'.format( |
|
286
|
|
|
#### GO=self.id, L=self.level, D=self.depth, desc=self.name)) |
|
287
|
|
|
#### # Track GOs previously printed only if needed |
|
288
|
|
|
#### if short_prt: |
|
289
|
|
|
#### gos_printed.add(goid) |
|
290
|
|
|
#### # Do not print hierarchy below this turn if it has already been printed |
|
291
|
|
|
#### if nrp: |
|
292
|
|
|
#### return |
|
293
|
|
|
#### depth += 1 |
|
294
|
|
|
#### if max_depth is not None and depth > max_depth: |
|
295
|
|
|
#### return |
|
296
|
|
|
#### for child in self.children: |
|
297
|
|
|
#### child.write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, short_prt, |
|
298
|
|
|
#### include_only, go_marks, |
|
299
|
|
|
#### depth, depth_dashes) |
|
300
|
|
|
|
|
301
|
|
|
|
|
302
|
|
|
class GODag(dict): |
|
303
|
|
|
"""Holds the GO DAG as a dict.""" |
|
304
|
|
|
|
|
305
|
|
|
def __init__(self, obo_file="go-basic.obo", optional_attrs=None, load_obsolete=False, prt=sys.stdout): |
|
306
|
|
|
super(GODag, self).__init__() |
|
307
|
|
|
self.version = self.load_obo_file(obo_file, optional_attrs, load_obsolete, prt) |
|
308
|
|
|
|
|
309
|
|
|
def load_obo_file(self, obo_file, optional_attrs, load_obsolete, prt): |
|
310
|
|
|
"""Read obo file. Store results.""" |
|
311
|
|
|
reader = OBOReader(obo_file, optional_attrs) |
|
312
|
|
|
|
|
313
|
|
|
# Save alt_ids and their corresponding main GO ID. Add to GODag after populating GO Terms |
|
314
|
|
|
alt2rec = {} |
|
315
|
|
|
for rec in reader: |
|
316
|
|
|
# Save record if: |
|
317
|
|
|
# 1) Argument load_obsolete is True OR |
|
318
|
|
|
# 2) Argument load_obsolete is False and the GO term is "live" (not obsolete) |
|
319
|
|
|
if load_obsolete or not rec.is_obsolete: |
|
320
|
|
|
self[rec.id] = rec |
|
321
|
|
|
for alt in rec.alt_ids: |
|
322
|
|
|
alt2rec[alt] = rec |
|
323
|
|
|
|
|
324
|
|
|
# Save the typedefs and parsed optional_attrs |
|
325
|
|
|
# self.optobj = reader.optobj |
|
326
|
|
|
self.typedefs = reader.typedefs |
|
327
|
|
|
|
|
328
|
|
|
self._populate_terms(reader.optobj) |
|
329
|
|
|
self._set_level_depth(reader.optobj) |
|
330
|
|
|
|
|
331
|
|
|
# Add alt_ids to go2obj |
|
332
|
|
|
for goid_alt, rec in alt2rec.items(): |
|
333
|
|
|
self[goid_alt] = rec |
|
334
|
|
|
desc = self._str_desc(reader) |
|
335
|
|
|
if prt is not None: |
|
336
|
|
|
prt.write("{DESC}\n".format(DESC=desc)) |
|
337
|
|
|
return desc |
|
338
|
|
|
|
|
339
|
|
|
def _str_desc(self, reader): |
|
340
|
|
|
"""String containing information about the current GO DAG.""" |
|
341
|
|
|
data_version = reader.data_version |
|
342
|
|
|
if data_version is not None: |
|
343
|
|
|
data_version = data_version.replace("releases/", "") |
|
344
|
|
|
desc = "{OBO}: fmt({FMT}) rel({REL}) {N:,} GO Terms".format( |
|
345
|
|
|
OBO=reader.obo_file, FMT=reader.format_version, |
|
346
|
|
|
REL=data_version, N=len(self)) |
|
347
|
|
|
if reader.optobj: |
|
348
|
|
|
desc = "{D}; optional_attrs({A})".format(D=desc, A=" ".join(sorted(reader.optobj.optional_attrs))) |
|
349
|
|
|
return desc |
|
350
|
|
|
|
|
351
|
|
|
|
|
352
|
|
|
def _populate_terms(self, optobj): |
|
353
|
|
|
"""Convert GO IDs to GO Term record objects. Populate children.""" |
|
354
|
|
|
has_relationship = optobj is not None and 'relationship' in optobj.optional_attrs |
|
355
|
|
|
# Make parents and relationships references to the actual GO terms. |
|
356
|
|
|
for rec in self.values(): |
|
357
|
|
|
# Given parent GO IDs, set parent GO Term objects |
|
358
|
|
|
rec.parents = set([self[goid] for goid in rec._parents]) |
|
359
|
|
|
|
|
360
|
|
|
# For each parent GO Term object, add it's child GO Term to the children data member |
|
361
|
|
|
for parent_rec in rec.parents: |
|
362
|
|
|
parent_rec.children.add(rec) |
|
363
|
|
|
|
|
364
|
|
|
if has_relationship: |
|
365
|
|
|
self._populate_relationships(rec) |
|
366
|
|
|
|
|
367
|
|
|
def _populate_relationships(self, rec_curr): |
|
368
|
|
|
"""Convert GO IDs in relationships to GO Term record objects. Populate children.""" |
|
369
|
|
|
for relationship_type, goids in rec_curr.relationship.items(): |
|
370
|
|
|
parent_recs = set([self[goid] for goid in goids]) |
|
371
|
|
|
rec_curr.relationship[relationship_type] = parent_recs |
|
372
|
|
|
for parent_rec in parent_recs: |
|
373
|
|
|
if relationship_type not in parent_rec.relationship_rev: |
|
374
|
|
|
parent_rec.relationship_rev[relationship_type] = set([rec_curr]) |
|
375
|
|
|
else: |
|
376
|
|
|
parent_rec.relationship_rev[relationship_type].add(rec_curr) |
|
377
|
|
|
|
|
378
|
|
|
def _set_level_depth(self, optobj): |
|
379
|
|
|
"""Set level, depth and add inverted relationships.""" |
|
380
|
|
|
has_relationship = optobj is not None and 'relationship' in optobj.optional_attrs |
|
381
|
|
|
|
|
382
|
|
|
def _init_level(rec): |
|
383
|
|
|
if rec.level is None: |
|
384
|
|
|
if rec.parents: |
|
385
|
|
|
rec.level = min(_init_level(rec) for rec in rec.parents) + 1 |
|
386
|
|
|
else: |
|
387
|
|
|
rec.level = 0 |
|
388
|
|
|
return rec.level |
|
389
|
|
|
|
|
390
|
|
|
def _init_depth(rec): |
|
391
|
|
|
if rec.depth is None: |
|
392
|
|
|
if rec.parents: |
|
393
|
|
|
rec.depth = max(_init_depth(rec) for rec in rec.parents) + 1 |
|
394
|
|
|
else: |
|
395
|
|
|
rec.depth = 0 |
|
396
|
|
|
return rec.depth |
|
397
|
|
|
|
|
398
|
|
|
def _init_reldepth(rec): |
|
399
|
|
|
if not hasattr(rec, 'reldepth'): |
|
400
|
|
|
up_terms = rec.get_goterms_upper() |
|
401
|
|
|
if up_terms: |
|
402
|
|
|
rec.reldepth = max(_init_reldepth(rec) for rec in up_terms) + 1 |
|
403
|
|
|
else: |
|
404
|
|
|
rec.reldepth = 0 |
|
405
|
|
|
return rec.reldepth |
|
406
|
|
|
|
|
407
|
|
|
for rec in self.values(): |
|
408
|
|
|
|
|
409
|
|
|
# Add invert relationships |
|
410
|
|
|
if has_relationship: |
|
411
|
|
|
if rec.depth is None: |
|
412
|
|
|
_init_reldepth(rec) |
|
413
|
|
|
|
|
414
|
|
|
# print("BBBBBBBBBBB1", rec.id, rec.relationship) |
|
415
|
|
|
#for (typedef, terms) in rec.relationship.items(): |
|
416
|
|
|
# invert_typedef = self.typedefs[typedef].inverse_of |
|
417
|
|
|
# # print("BBBBBBBBBBB2 {} ({}) ({}) ({})".format( |
|
418
|
|
|
# # rec.id, rec.relationship, typedef, invert_typedef)) |
|
419
|
|
|
# if invert_typedef: |
|
420
|
|
|
# # Add inverted relationship |
|
421
|
|
|
# for term in terms: |
|
422
|
|
|
# if not hasattr(term, 'relationship'): |
|
423
|
|
|
# term.relationship = defaultdict(set) |
|
424
|
|
|
# term.relationship[invert_typedef].add(rec) |
|
425
|
|
|
# print("BBBBBBBBBBB3", rec.id, rec.relationship) |
|
426
|
|
|
|
|
427
|
|
|
if rec.level is None: |
|
428
|
|
|
_init_level(rec) |
|
429
|
|
|
|
|
430
|
|
|
if rec.depth is None: |
|
431
|
|
|
_init_depth(rec) |
|
432
|
|
|
|
|
433
|
|
|
def write_dag(self, out=sys.stdout): |
|
434
|
|
|
"""Write info for all GO Terms in obo file, sorted numerically.""" |
|
435
|
|
|
for rec in sorted(self.values()): |
|
436
|
|
|
print(rec, file=out) |
|
437
|
|
|
|
|
438
|
|
|
#### def write_hier_all(self, out=sys.stdout, |
|
439
|
|
|
#### len_dash=1, max_depth=None, num_child=None, short_prt=False): |
|
440
|
|
|
#### """Write hierarchy for all GO Terms in obo file.""" |
|
441
|
|
|
#### # Print: [biological_process, molecular_function, and cellular_component] |
|
442
|
|
|
#### for go_id in ['GO:0008150', 'GO:0003674', 'GO:0005575']: |
|
443
|
|
|
#### self.write_hier(go_id, out, len_dash, max_depth, num_child, short_prt, None) |
|
444
|
|
|
#### |
|
445
|
|
|
#### def write_hier(self, go_id, out=sys.stdout, |
|
446
|
|
|
#### len_dash=1, max_depth=None, num_child=None, short_prt=False, |
|
447
|
|
|
#### include_only=None, go_marks=None): |
|
448
|
|
|
#### """Write hierarchy for a GO Term.""" |
|
449
|
|
|
#### gos_printed = set() |
|
450
|
|
|
#### self[go_id].write_hier_rec(gos_printed, out, len_dash, max_depth, num_child, |
|
451
|
|
|
#### short_prt, include_only, go_marks) |
|
452
|
|
|
|
|
453
|
|
|
@staticmethod |
|
454
|
|
|
def id2int(go_id): |
|
455
|
|
|
"""Given a GO ID, return the int value.""" |
|
456
|
|
|
return int(go_id.replace("GO:", "", 1)) |
|
457
|
|
|
|
|
458
|
|
|
def query_term(self, term, verbose=False): |
|
459
|
|
|
"""Given a GO ID, return GO object.""" |
|
460
|
|
|
if term not in self: |
|
461
|
|
|
sys.stderr.write("Term %s not found!\n" % term) |
|
462
|
|
|
return |
|
463
|
|
|
|
|
464
|
|
|
rec = self[term] |
|
465
|
|
|
if verbose: |
|
466
|
|
|
print(rec) |
|
467
|
|
|
sys.stderr.write("all parents: {}\n".format( |
|
468
|
|
|
repr(rec.get_all_parents()))) |
|
469
|
|
|
sys.stderr.write("all children: {}\n".format( |
|
470
|
|
|
repr(rec.get_all_children()))) |
|
471
|
|
|
return rec |
|
472
|
|
|
|
|
473
|
|
|
def paths_to_top(self, term): |
|
474
|
|
|
""" Returns all possible paths to the root node |
|
475
|
|
|
|
|
476
|
|
|
Each path includes the term given. The order of the path is |
|
477
|
|
|
top -> bottom, i.e. it starts with the root and ends with the |
|
478
|
|
|
given term (inclusively). |
|
479
|
|
|
|
|
480
|
|
|
Parameters: |
|
481
|
|
|
----------- |
|
482
|
|
|
- term: |
|
483
|
|
|
the id of the GO term, where the paths begin (i.e. the |
|
484
|
|
|
accession 'GO:0003682') |
|
485
|
|
|
|
|
486
|
|
|
Returns: |
|
487
|
|
|
-------- |
|
488
|
|
|
- a list of lists of GO Terms |
|
489
|
|
|
""" |
|
490
|
|
|
# error handling consistent with original authors |
|
491
|
|
|
if term not in self: |
|
492
|
|
|
sys.stderr.write("Term %s not found!\n" % term) |
|
493
|
|
|
return |
|
494
|
|
|
|
|
495
|
|
|
def _paths_to_top_recursive(rec): |
|
496
|
|
|
if rec.level == 0: |
|
497
|
|
|
return [[rec]] |
|
498
|
|
|
paths = [] |
|
499
|
|
|
for parent in rec.parents: |
|
500
|
|
|
top_paths = _paths_to_top_recursive(parent) |
|
501
|
|
|
for top_path in top_paths: |
|
502
|
|
|
top_path.append(rec) |
|
503
|
|
|
paths.append(top_path) |
|
504
|
|
|
return paths |
|
505
|
|
|
|
|
506
|
|
|
go_term = self[term] |
|
507
|
|
|
return _paths_to_top_recursive(go_term) |
|
508
|
|
|
|
|
509
|
|
|
def label_wrap(self, label): |
|
510
|
|
|
"""Label text for plot.""" |
|
511
|
|
|
wrapped_label = r"%s\n%s" % (label, |
|
512
|
|
|
self[label].name.replace(",", r"\n")) |
|
513
|
|
|
return wrapped_label |
|
514
|
|
|
|
|
515
|
|
|
def make_graph_pydot(self, recs, nodecolor, |
|
516
|
|
|
edgecolor, dpi, |
|
517
|
|
|
draw_parents=True, draw_children=True): |
|
518
|
|
|
"""draw AMIGO style network, lineage containing one query record.""" |
|
519
|
|
|
import pydot |
|
520
|
|
|
grph = pydot.Dot(graph_type='digraph', dpi="{}".format(dpi)) # Directed Graph |
|
521
|
|
|
edgeset = set() |
|
522
|
|
|
usr_ids = [rec.id for rec in recs] |
|
523
|
|
|
for rec in recs: |
|
524
|
|
|
if draw_parents: |
|
525
|
|
|
edgeset.update(rec.get_all_parent_edges()) |
|
526
|
|
|
if draw_children: |
|
527
|
|
|
edgeset.update(rec.get_all_child_edges()) |
|
528
|
|
|
|
|
529
|
|
|
rec_id_set = set([rec_id for endpts in edgeset for rec_id in endpts]) |
|
530
|
|
|
nodes = {str(ID):pydot.Node( |
|
531
|
|
|
self.label_wrap(ID).replace("GO:", ""), # Node name |
|
532
|
|
|
shape="box", |
|
533
|
|
|
style="rounded, filled", |
|
534
|
|
|
# Highlight query terms in plum: |
|
535
|
|
|
fillcolor="beige" if ID not in usr_ids else "plum", |
|
536
|
|
|
color=nodecolor) |
|
537
|
|
|
for ID in rec_id_set} |
|
538
|
|
|
|
|
539
|
|
|
# add nodes explicitly via add_node |
|
540
|
|
|
for rec_id, node in nodes.items(): |
|
541
|
|
|
grph.add_node(node) |
|
542
|
|
|
|
|
543
|
|
|
for src, target in edgeset: |
|
544
|
|
|
# default layout in graphviz is top->bottom, so we invert |
|
545
|
|
|
# the direction and plot using dir="back" |
|
546
|
|
|
grph.add_edge(pydot.Edge(nodes[target], nodes[src], |
|
547
|
|
|
shape="normal", |
|
548
|
|
|
color=edgecolor, |
|
549
|
|
|
label="is_a", |
|
550
|
|
|
dir="back")) |
|
551
|
|
|
|
|
552
|
|
|
return grph |
|
553
|
|
|
|
|
554
|
|
|
def make_graph_pygraphviz(self, recs, nodecolor, |
|
555
|
|
|
edgecolor, dpi, |
|
556
|
|
|
draw_parents=True, draw_children=True): |
|
557
|
|
|
"""Draw AMIGO style network, lineage containing one query record.""" |
|
558
|
|
|
import pygraphviz as pgv |
|
559
|
|
|
|
|
560
|
|
|
grph = pgv.AGraph(name="GO tree") |
|
561
|
|
|
|
|
562
|
|
|
edgeset = set() |
|
563
|
|
|
for rec in recs: |
|
564
|
|
|
if draw_parents: |
|
565
|
|
|
edgeset.update(rec.get_all_parent_edges()) |
|
566
|
|
|
if draw_children: |
|
567
|
|
|
edgeset.update(rec.get_all_child_edges()) |
|
568
|
|
|
|
|
569
|
|
|
edgeset = [(self.label_wrap(a), self.label_wrap(b)) |
|
570
|
|
|
for (a, b) in edgeset] |
|
571
|
|
|
|
|
572
|
|
|
# add nodes explicitly via add_node |
|
573
|
|
|
# adding nodes implicitly via add_edge misses nodes |
|
574
|
|
|
# without at least one edge |
|
575
|
|
|
for rec in recs: |
|
576
|
|
|
grph.add_node(self.label_wrap(rec.id)) |
|
577
|
|
|
|
|
578
|
|
|
for src, target in edgeset: |
|
579
|
|
|
# default layout in graphviz is top->bottom, so we invert |
|
580
|
|
|
# the direction and plot using dir="back" |
|
581
|
|
|
grph.add_edge(target, src) |
|
582
|
|
|
|
|
583
|
|
|
grph.graph_attr.update(dpi="%d" % dpi) |
|
584
|
|
|
grph.node_attr.update(shape="box", style="rounded,filled", |
|
585
|
|
|
fillcolor="beige", color=nodecolor) |
|
586
|
|
|
grph.edge_attr.update(shape="normal", color=edgecolor, |
|
587
|
|
|
dir="back", label="is_a") |
|
588
|
|
|
# highlight the query terms |
|
589
|
|
|
for rec in recs: |
|
590
|
|
|
try: |
|
591
|
|
|
node = grph.get_node(self.label_wrap(rec.id)) |
|
592
|
|
|
node.attr.update(fillcolor="plum") |
|
593
|
|
|
except: |
|
594
|
|
|
continue |
|
595
|
|
|
|
|
596
|
|
|
return grph |
|
597
|
|
|
|
|
598
|
|
|
def draw_lineage(self, recs, nodecolor="mediumseagreen", |
|
599
|
|
|
edgecolor="lightslateblue", dpi=96, |
|
600
|
|
|
lineage_img="GO_lineage.png", engine="pygraphviz", |
|
601
|
|
|
gml=False, draw_parents=True, draw_children=True): |
|
602
|
|
|
"""Draw GO DAG subplot.""" |
|
603
|
|
|
assert engine in GraphEngines |
|
604
|
|
|
grph = None |
|
605
|
|
|
if engine == "pygraphviz": |
|
606
|
|
|
grph = self.make_graph_pygraphviz(recs, nodecolor, edgecolor, dpi, |
|
607
|
|
|
draw_parents=draw_parents, |
|
608
|
|
|
draw_children=draw_children) |
|
609
|
|
|
else: |
|
610
|
|
|
grph = self.make_graph_pydot(recs, nodecolor, edgecolor, dpi, |
|
611
|
|
|
draw_parents=draw_parents, draw_children=draw_children) |
|
612
|
|
|
|
|
613
|
|
|
if gml: |
|
614
|
|
|
import networkx as nx # use networkx to do the conversion |
|
615
|
|
|
gmlbase = lineage_img.rsplit(".", 1)[0] |
|
616
|
|
|
obj = nx.from_agraph(grph) if engine == "pygraphviz" else nx.from_pydot(grph) |
|
617
|
|
|
|
|
618
|
|
|
del obj.graph['node'] |
|
619
|
|
|
del obj.graph['edge'] |
|
620
|
|
|
gmlfile = gmlbase + ".gml" |
|
621
|
|
|
nx.write_gml(self.label_wrap, gmlfile) |
|
622
|
|
|
sys.stderr.write("GML graph written to {0}\n".format(gmlfile)) |
|
623
|
|
|
|
|
624
|
|
|
sys.stderr.write(("lineage info for terms %s written to %s\n" % |
|
625
|
|
|
([rec.id for rec in recs], lineage_img))) |
|
626
|
|
|
|
|
627
|
|
|
if engine == "pygraphviz": |
|
628
|
|
|
grph.draw(lineage_img, prog="dot") |
|
629
|
|
|
else: |
|
630
|
|
|
grph.write_png(lineage_img) |
|
631
|
|
|
|
|
632
|
|
|
def update_association(self, association): |
|
633
|
|
|
"""Add the GO parents of a gene's associated GO IDs to the gene's association.""" |
|
634
|
|
|
bad_goids = set() |
|
635
|
|
|
# Loop through all sets of GO IDs for all genes |
|
636
|
|
|
for goids in association.values(): |
|
637
|
|
|
parents = set() |
|
638
|
|
|
# Iterate thru each GO ID in the current gene's association |
|
639
|
|
|
for goid in goids: |
|
640
|
|
|
try: |
|
641
|
|
|
parents.update(self[goid].get_all_parents()) |
|
642
|
|
|
except: |
|
643
|
|
|
bad_goids.add(goid.strip()) |
|
644
|
|
|
# Add the GO parents of all GO IDs in the current gene's association |
|
645
|
|
|
goids.update(parents) |
|
646
|
|
|
if bad_goids: |
|
647
|
|
|
sys.stdout.write("{N} GO IDs in assc. are not found in the GO-DAG: {GOs}\n".format( |
|
648
|
|
|
N=len(bad_goids), GOs=" ".join(bad_goids))) |
|
649
|
|
|
|
|
650
|
|
|
# Copyright (C) 2010-2018, H Tang et al., All rights reserved. |
|
651
|
|
|
|
tanghaibao /
goatools
