def render(self, graphics, ypos, rng, style, error):
from random import random
data = []
for i in range(0, 120):
data.append(random())
graphics.draw_curve_data(graphics.get_xmargins(), ypos,
Color(0, 0, 1, .6), data, 120, Range(0, 1),
40)
return 0
def get_range_for_seqid(self, seqid):
from ctypes import byref
err = Error()
if self.has_seqid(seqid) == 0:
gterror("feature_index does not contain seqid")
range = Range()
rval = gtlib.gt_feature_index_get_range_for_seqid(
self.fi, byref(range), seqid.encode('UTF-8'), err)
if rval != 0:
gterror(err)
return range
def get_features_for_range(self, start, end, seqid):
from ctypes import byref
a = Array.create()
err = Error()
rng = Range(start, end)
rval = gtlib.gt_feature_index_get_features_for_range(
self.fi, a, seqid, byref(rng), err)
if rval != 0:
gterror(err)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
# 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)
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)
nodes.append(reverse_gene)
pngfile = (sys.argv)[2]
style = Style()
style.load_file((sys.argv)[1])
diagram = Diagram.from_array(nodes, Range(G.start, G.end), style)
layout = Layout(diagram, 600, style)
height = layout.get_height()
canvas = CanvasCairoFile(style, 600, height)
layout.sketch(canvas)
canvas.to_file(pngfile)