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
|
#!/usr/bin/python3
"""
annotate a file with the nearest features in another.
%prog [options]
if --upstream and --downstream are not specified only 2 colummns are
added to the [a] file: nearest_name, nearest_distance.
if they are specified upstream_names, downstream_names are specified.
if --report-distance is included, the format will be:
gene:dist,gene2:dist2
for each of the up and downstream columns.
"""
import argparse
import sys
from pybedtools import BedTool
from pybedtools.cbedtools import Attributes
import collections
# PYTHONPATH=$PYTHONPATH:. python scripts/annotate.py -a data/new.regions.bed
# -b data/Homo_sapiens.hg18.gtf --upstream 5000
# $ pybedtools annotate -a regions.bed -b knownGene.bed --upstream 10000
# --downstream 5000 --report-distance
# a bed: regions.bed and another:
# annotation.bed, it would add 4 columns to regions.bed:
# nearest-feature, nearest-distance, upstream-features, downstream-features
# where the up/downstream features are determined by a distance
# parameter, e.g. like --upstream 10000 --downstream 5000
def get_gff_name(field):
attrs = Attributes(field)
for key in ("ID", "gene_name", "transcript_id", "gene_id", "Parent"):
if key in attrs:
return attrs[key]
def gen_get_name(b, afields):
btype = b.file_type
if btype == "bed":
get_name = lambda fields: fields[afields + 3]
elif btype == "gff":
def get_name(fields):
return get_gff_name(fields[afields + 7])
else:
raise Exception("not implemented")
return get_name
def add_closest(aname, bname):
a, b = BedTool(aname), BedTool(bname)
afields = a.field_count()
c = a.closest(b, d=True)
get_name = gen_get_name(b, afields)
dbed = open(BedTool._tmp(), "w")
# keep the name and distance
seen_by_line = collections.defaultdict(list)
for feat in c:
key = "\t".join(feat[:afields])
seen_by_line[key].append([feat[-1], get_name(feat)])
for key, dist_names in seen_by_line.items():
if len(dist_names) > 0:
assert len(set([d[0] for d in dist_names])) == 1
names = ",".join(sorted(set(d[1] for d in dist_names)))
new_line = "\t".join([key] + [names] + [dist_names[0][0]])
dbed.write(new_line + "\n")
dbed.close()
d = BedTool(dbed.name)
assert len(d) == len(a)
return d
def add_xstream(a, b, dist, updown, report_distance=False):
# run a window up or downstream.
dir = dict(up="l", down="r")[updown]
kwargs = {"sw": True, dir: dist}
# have to set the other to 0
if "l" in kwargs:
kwargs["r"] = 0
else:
kwargs["l"] = 0
c = a.window(b, **kwargs)
afields = a.field_count()
get_name = gen_get_name(b, afields)
seen = collections.defaultdict(set)
# condense to unique names.
for row in c:
key = "\t".join(row[:afields])
seen[key].update([get_name(row)])
d = open(BedTool._tmp(), "w")
for row in seen:
d.write(row + "\t" + ",".join(sorted(seen[row])) + "\n")
# write the entries that did not appear in the window'ed Bed
for row in a:
key = "\t".join(row[:afields])
if key in seen:
continue
d.write(str(row) + "\t.\n")
d.close()
dbed = BedTool(d.name)
assert len(dbed) == len(a)
return dbed
def main():
"""
annotate a file with the nearest features in another.
"""
p = argparse.ArgumentParser(description=__doc__, prog=sys.argv[0])
p.add_argument("-a", dest="a", help="file to annotate")
p.add_argument("-b", dest="b", help="file with annotations")
p.add_argument(
"--upstream",
dest="upstream",
type=int,
default=None,
help="distance upstream of [a] to look for [b]",
)
p.add_argument(
"--downstream",
dest="downstream",
type=int,
default=None,
help="distance downstream of [a] to look for [b]",
)
p.add_argument(
"--report-distance",
dest="report_distance",
default=False,
help="report the distance, not just the genes",
action="store_true",
)
args = p.parse_args()
if args.a is None or args.b is None:
sys.exit(not p.print_help())
c = add_closest(args.a, args.b)
b = BedTool(args.b)
# TODO: support --report-distance for up/downstream.
if args.upstream:
c = add_xstream(c, b, args.upstream, "up", args.report_distance)
if args.downstream:
c = add_xstream(c, b, args.downstream, "down", args.report_distance)
for row in c.sort():
print(row)
if __name__ == "__main__":
import doctest
if doctest.testmod(optionflags=doctest.ELLIPSIS).failed == 0:
main()
|
