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
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re
if __name__ == "__main__":
if len(sys.argv) != 3:
sys.stderr.write("Usage: " + (sys.argv)[0] +
" PNG_file GFF3_file\n")
sys.stderr.write("Create PNG representation of GFF3 annotation file (adds introns).")
sys.exit(1)
pngfile = (sys.argv)[1]
in_stream = GFF3InStream((sys.argv)[2])
add_introns_stream = AddIntronsStream(in_stream)
feature_index = FeatureIndexMemory()
feature_stream = FeatureStream(add_introns_stream, feature_index)
gn = feature_stream.next_tree()
# fill feature index
while gn:
gn = feature_stream.next_tree()
seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)
style = Style()
diagram = Diagram.from_index(feature_index, seqid, range, style)
layout = Layout(diagram, 700, style)
height = layout.get_height()
ii = ImageInfo()
canvas = CanvasCairoFile(style, 700, height, ii)
layout.sketch(canvas)
pngstream = canvas.to_stream()
outfile = open(pngfile, "wb")
outfile.write(pngstream)
outfile.close()
|
