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
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
|
"""
Convert GTF to bed12, bed6, intron and etc..
Author: liqiming@whu.edu.cn
"""
import re
import argparse
from itertools import groupby
def reader(fname, header=None, sep="\t", skip_while=None):
sep = re.compile(sep)
with open(fname) as f:
for line in f:
toks = sep.split(line.rstrip("\r\n"))
if skip_while:
if skip_while(toks):
continue
if header:
yield header(toks)
else:
yield toks
def parse_attributes(term, attributes):
parse_attr = re.compile('{term} "([^"]+)"'.format(term=term))
patterns = parse_attr.findall(attributes)
if patterns:
return patterns[0]
else:
return 'NA'
class Alias:
def __init__(self, data):
self.data = data
def update(self, data):
self.data = data
def __repr__(self):
return str(self.data)
__str__ = __repr__
class TransInfo:
"""Get transcript info"""
__slots__ = ["transcript_id", "transcript_name", "transcript_type",
"gene_id", "gene_name", "gene_type", "strand"]
def __init__(self, gtf, attr):
self.strand = gtf.strand
attributes = gtf.attributes
self.transcript_id = attr
self.transcript_name = parse_attributes("transcript_name", attributes)
self.transcript_type = parse_attributes("transcript_type", attributes)
self.gene_id = parse_attributes("gene_id", attributes)
self.gene_name = parse_attributes("gene_name", attributes)
self.gene_type = parse_attributes("gene_type", attributes)
def __repr__(self):
return "Transcript({transcript_id} {transcript_type} {strand})".format(
transcript_id=self.transcript_id,
transcript_type=self.transcript_type,
strand=self.strand
)
def __str__(self):
return "\t".join(str(getattr(self, s)) for s in self.__slots__)
class GeneInfo:
"""Get gene info"""
__slots__ = ["gene_id", "gene_name", "gene_type", "strand"]
def __init__(self, gtf, attr):
self.strand = gtf.strand
attributes = gtf.attributes
self.gene_id = attr
self.gene_name = parse_attributes("gene_name", attributes)
self.gene_type = parse_attributes("gene_type", attributes)
def __repr__(self):
return "Gene({gene_id} {gene_type} {strand})".format(
gene_id=self.gene_id,
gene_type=self.gene_type,
strand=self.strand
)
def __str__(self):
return "\t".join(str(getattr(self, s)) for s in self.__slots__)
class Bed6:
"""Convert GTF to Bed6."""
__slots__ = ["chrom", "start", "end", "name", "score", "strand"]
def __init__(self, gtf, attr):
self.chrom = gtf.chrom
self.start = gtf.start - 1
self.end = gtf.end
self.name = attr
self.score = gtf.score
self.strand = gtf.strand
def __repr__(self):
return "Bed6({chrom}:{start}-{end})".format(
chrom=self.chrom, start=self.start, end=self.end)
def __str__(self):
return "\t".join(str(getattr(self, s)) for s in self.__slots__)
class Bed12:
"""Convert GTF to Bed12."""
__slots__ = ["chrom", "start", "end", "name", "score", "strand",
"thickStart", "thickEnd", "itemRgb", "blockCount",
"blockSizes", "blockStarts"]
def __init__(self, gtf, attr, thickStart, thickEnd):
self.chrom = gtf.chrom
self.start = gtf.start - 1
self.end = Alias(gtf.end)
self.name = attr
self.score = 0 if gtf.score == '.' else int(gtf.score)
self.strand = gtf.strand
if thickStart and thickEnd:
self.thickStart = thickStart
self.thickEnd = thickEnd
else:
self.thickStart = self.end
self.thickEnd = self.end
self.itemRgb = 0
self.blockCount = 1
self.blockSizes = "{size},".format(size=gtf.end - gtf.start + 1)
self.blockStarts = "{start},".format(start=0)
def __repr__(self):
return "Bed12({chrom}:{start}-{end})".format(
chrom=self.chrom, start=self.start, end=self.end)
def __str__(self):
return "\t".join(str(getattr(self, s)) for s in self.__slots__)
def add_exon(self, gtf):
self.end.update(gtf.end)
self.blockSizes += "{size},".format(size=gtf.end - gtf.start + 1)
self.blockStarts += "{start},".format(start=gtf.start - 1 - self.start)
self.blockCount += 1
class Intron:
"""Convert GTF to Intron Bed6."""
__slots__ = ["chrom", "start", "end", "name", "score", "strand"]
def __init__(self, exon_1, exon_2, attr):
self.chrom = exon_1.chrom
self.start = exon_1.end
self.end = exon_2.start - 1
assert self.end >= self.start
self.name = attr
self.score = '.'
self.strand = exon_1.strand
def __repr__(self):
return "Intron({chrom}:{start}-{end})".format(
chrom=self.chrom, start=self.start, end=self.end)
def __str__(self):
return "\t".join(str(getattr(self, s)) for s in self.__slots__)
class GTF:
__slots__ = ['seqname', 'source', 'feature', 'start', 'end', 'score',
'strand', 'frame', 'attributes', 'chrom']
def __init__(self, args):
for s, v in zip(self.__slots__[:9], args):
setattr(self, s, v)
self.start = int(self.start)
self.end = int(self.end)
self.chrom = self.seqname
def __repr__(self):
return "GTF({seqname}:{start}-{end})".format(
seqname=self.seqname, start=self.start, end=self.end)
def main(gtf, attribute_id, feature, outformat):
assert outformat in (
"bed12", "bed6", "intron", "info"
), "output file format: {} not support.".format(outformat)
parse_attr = re.compile(
'{attribute_id} "([^"]+)"'.format(attribute_id=attribute_id))
if outformat == 'bed12':
cds = dict()
for k, group in groupby(
reader(
gtf,
header=GTF,
skip_while=lambda toks: toks[0].startswith("#") or not (
toks[2] == 'CDS' or toks[2] == 'stop_codon')
),
lambda x: parse_attr.findall(x.attributes)[0]
):
gtfs = list(sorted(group, key=lambda gtf: gtf.start))
thickStart = gtfs[0].start - 1
thickEnd = gtfs[-1].end
cds[k] = (thickStart, thickEnd)
if outformat == 'info':
if attribute_id == 'transcript_id':
head = ["transcript_id", "transcript_name", "transcript_type",
"gene_id", "gene_name", "gene_type", "strand"]
print("\t".join(head))
elif attribute_id == 'gene_id':
head = ["gene_id", "gene_name", "gene_type", "strand"]
print("\t".join(head))
else:
raise Exception("GTF attribute and outformat not support.")
for k, group in groupby(
reader(
gtf,
header=GTF,
skip_while=lambda toks: toks[0].startswith("#") or not (
toks[2] == feature)
),
lambda x: parse_attr.findall(x.attributes)[0]
):
if outformat == 'bed12':
bed = None
for gtf_entry in sorted(group, key=lambda gtf: gtf.start):
if not bed:
try:
thickStart, thickEnd = cds[k]
except Exception:
thickStart = thickEnd = None
bed = Bed12(gtf_entry, k, thickStart, thickEnd)
else:
bed.add_exon(gtf_entry)
print(bed)
elif outformat == 'bed6':
for gtf_entry in group:
bed = Bed6(gtf_entry, k)
print(bed)
elif outformat == 'intron':
exons = []
for gtf_entry in sorted(group, key=lambda gtf: gtf.start):
exons.append(gtf_entry)
assert len(exons) > 0
if len(exons) < 2:
continue
for i in range(len(exons) - 1):
intron = Intron(exons[i], exons[i+1], k)
print(intron)
elif outformat == 'info' and attribute_id == 'transcript_id':
for gtf_entry in group:
transcript_info = TransInfo(gtf_entry, k)
print(transcript_info)
elif outformat == 'info' and attribute_id == 'gene_id':
for gtf_entry in group:
gene_info = GeneInfo(gtf_entry, k)
print(gene_info)
if __name__ == '__main__':
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p.add_argument('gtf', help="gtf file download from Genecode.")
p.add_argument('--attribute', dest='attr', default='transcript_id', help="""
attribute ID by which to group bed entries.
'gene_id' or 'gene_name' for gene.bed6, gene_info
'transcript_id' for genome.bed12, exon, intron, transcrpt_info
""")
p.add_argument('--type', dest='feature', default='exon', help="""
annotation type to join, all others are filtered out:
'exon' genome.bed12, exon, intron, 'gene' for gene.bed6, gene_info,
'transcript' for transcript_info.
""")
p.add_argument('--format', dest='outformat', default='bed12', help="""
choose output file format:bed12, bed6, intron, info
""")
args = p.parse_args()
main(args.gtf, args.attr, args.feature, args.outformat)
|
