def test_no_stack_at_all(self):
seq = self.genome["chrI"]
annots = {}
annots["a"] = pygr_draw.Annotation("a", "chrI", 0, 50)
map = pygr_draw.create_annotation_map(annots, self.genome)
slots = pygr_draw.stack_annotations(seq, map)
assert slots["a"] == 0 # should be on level 0
def test_stack_two(self):
seq = self.genome["chrI"]
annots = {}
annots["a"] = pygr_draw.Annotation("a", "chrI", 0, 50)
annots["b"] = pygr_draw.Annotation("b", "chrI", 35, 100)
map = pygr_draw.create_annotation_map(annots, self.genome)
slots = pygr_draw.stack_annotations(seq, map)
assert slots["a"] == 1 # the short annot should be on level 1
assert slots["b"] == 0
def test_stack_many(self):
seq = self.genome["chrI"]
annots = {}
length = len(seq)
for i in range(0, length, 100):
name = "annot%d" % (i,)
annots[name] = pygr_draw.Annotation(name, "chrI", i, length)
map = pygr_draw.create_annotation_map(annots, self.genome)
slots = pygr_draw.stack_annotations(seq, map)
assert max(slots.values()) == len(annots) - 1
from pygr import seqdb
genome = seqdb.BlastDB('example.fa')
sequence_name = 'chrI'
import pygr_draw
from pygr_draw import AnnotationGroup, Annotation
picture_class = pygr_draw.BitmapSequencePicture
colors = picture_class.colors
annotations2 = {}
annotations2['blip'] = Annotation('blip', sequence_name, 25, 75, color=colors.green)
annotations2['gene1'] = AnnotationGroup('gene1', sequence_name, ((50, 100), (200, 300), (500, 1500)),color=colors.red)
annotations2['gene2'] = AnnotationGroup('gene2', sequence_name, ((100, 300), (1500, 2000), (3000, 3750)),color=colors.blue)
annotations2['gene3'] = AnnotationGroup('gene3', sequence_name, ((3800, 4000), (
4500, 5000)),color=colors.blue)
annotations_map = pygr_draw.create_annotation_map(annotations2, genome)
p = pygr_draw.draw_annotation_maps(genome[sequence_name][:4000],(annotations_map,),picture_class=picture_class)
image = p.finalize()
filename = 'group-example.png'
open(filename, 'w').write(image)
print 'Output in', filename
