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
|
#!/usr/bin/python
# -*- coding: utf-8 -*-
from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
from gt.annotationsketch.custom_track import CustomTrack
from gt.core.gtrange import Range
import sys
if __name__ == "__main__":
if len(sys.argv) != 3:
sys.stderr.write("Usage: " + (sys.argv)[0] +
" style_file PNG_file\n")
sys.exit(1)
seqid = "chromosome_21"
nodes = []
# construct a gene on the forward strand with two exons
gene = FeatureNode.create_new(seqid, "gene", 100, 900, "+")
exon = FeatureNode.create_new(seqid, "exon", 100, 200, "+")
gene.add_child(exon)
intron = FeatureNode.create_new(seqid, "intron", 201, 799, "+")
gene.add_child(intron)
exon = FeatureNode.create_new(seqid, "exon", 800, 900, "+")
gene.add_child(exon)
# construct a single-exon gene on the reverse strand
# (within the intron of the forward strand gene)
reverse_gene = FeatureNode.create_new(seqid, "gene", 400, 600, "-")
reverse_exon = FeatureNode.create_new(seqid, "exon", 400, 600, "-")
reverse_gene.add_child(reverse_exon)
pngfile = (sys.argv)[2]
style = Style()
style.load_file((sys.argv)[1])
diagram = Diagram.from_array([gene, reverse_gene], Range(1, 1000),
style)
layout = Layout(diagram, 600, style)
height = layout.get_height()
canvas = CanvasCairoFile(style, 600, height)
layout.sketch(canvas)
canvas.to_file(pngfile)
|
