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#!/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
class GeneRegion(object):
"""Represents a gene region"""
def __init__(self, start, end):
self.start = start
self.end = end
class BetterGeneRegion(GeneRegion):
"""Has even more info and inherits from GeneRegion"""
def __init__(self, start, end, chromosome, strand):
GeneRegion.__init__(self, start, end)
self.chromosome = chromosome
self.strand = strand
if __name__ == "__main__":
if len(sys.argv) != 3:
sys.stderr.write("Usage: " + (sys.argv)[0] +
" style_file PNG_file\n")
sys.exit(1)
# Strings in Python3 are always unicode and unicode() does not exist
# so there's no need to test this
if sys.version_info >= (3, 0):
sys.exit(0)
nodes = []
# construct a gene on the forward strand with two exons
G = BetterGeneRegion(113558120, 113578742, 'chr7', '+')
seqid = G.chromosome
gene = FeatureNode.create_new(unicode(seqid),
"gene",
#100,
#900,
G.start,
G.end,
"+")
# XXX FIXME: how to handle this case?
# gene.add_attribute("Name", "Testcase™ あがぃいぅ")
nodes.append(gene)
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)
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