def test_dict(self):
""" get_color_dict() for classes A-D, no jitter
"""
classes = ['A', 'B', 'C', 'D']
colors = get_color_dict(classes, jitter=0)
cstr = ["%s: (%.2f, %.2f, %.2f)" % (c, r, g, b)
for c, (r, g, b) in colors.items()]
expected = ['A: (0.52, 0.76, 0.69)', 'C: (0.59, 0.13, 0.47)',
'B: (0.40, 0.31, 0.68)', 'D: (0.50, 0.00, 0.00)']
self.assertEqual(cstr, expected)
def test_dict(self):
""" get_color_dict() for classes A-D, no jitter
"""
classes = ['A', 'B', 'C', 'D']
colors = get_color_dict(classes, jitter=0)
cstr = [
"%s: (%.2f, %.2f, %.2f)" % (c, r, g, b)
for c, (r, g, b) in colors.items()
]
expected = [
'A: (0.52, 0.76, 0.69)', 'C: (0.59, 0.13, 0.47)',
'B: (0.40, 0.31, 0.68)', 'D: (0.50, 0.00, 0.00)'
]
self.assertEqual(cstr, expected)
"DDA3937": (refdir, "NC_014500.gbk"),
"DDA3537": (gbkdir, "NCPPB_3537_draft.gbk"),
"DDI3534": (gbkdir, "NCPPB_3534_draft.gbk"),
"DDIIPO980": (gbkdir, "IPO_980_draft.gbk"),
"DDIGBBC2039": (gbkdir, "GBBC2039_draft.gbk"),
"DDI453": (gbkdir, "NCPPB_453_draft.gbk"),
}
# Create GenomeDiagram image
gdd = gd.Diagram("Dickeya core collinear regions", x=0.01, y=0.005)
tracks = {}
featuresets = {}
regionsets = {}
records = {}
track_level = 1
org_colours = get_color_dict(orgs, a=4)
for l, org in enumerate(orgs):
# Load data
filename = os.path.join(genome_data[org][0], genome_data[org][1])
print "Loading %s" % filename
records[org] = SeqIO.read(filename, "genbank")
if org in reverse:
print "Reverse-complementing %s" % org
records[org] = records[org].reverse_complement(annotations=True, id=True, name=True, description=True)
# Set up tracks
tracks[org] = gdd.new_track(
2 * l, name=org, greytrack=True, greytrack_labels=10, height=0.5, start=0, end=len(records[org])
)
regionsets[org] = tracks[org].new_set(name="collinear regions")
'DDA3937': (refdir, 'NC_014500.gbk'),
'DDA3537': (gbkdir, 'NCPPB_3537_draft.gbk'),
'DDI3534': (gbkdir, 'NCPPB_3534_draft.gbk'),
'DDIIPO980': (gbkdir, 'IPO_980_draft.gbk'),
'DDIGBBC2039': (gbkdir, 'GBBC2039_draft.gbk'),
'DDI453': (gbkdir, 'NCPPB_453_draft.gbk')
}
# Create GenomeDiagram image
gdd = gd.Diagram("Dickeya core collinear regions", x=0.01, y=0.005)
tracks = {}
featuresets = {}
regionsets = {}
records = {}
track_level = 1
org_colours = get_color_dict(orgs, a=4)
for l, org in enumerate(orgs):
# Load data
filename = os.path.join(genome_data[org][0], genome_data[org][1])
print "Loading %s" % filename
records[org] = SeqIO.read(filename, 'genbank')
if org in reverse:
print "Reverse-complementing %s" % org
records[org] = records[org].reverse_complement(annotations=True,
id=True, name=True,
description=True)
# Set up tracks
tracks[org] = gdd.new_track(2*l, name=org, greytrack=True,
greytrack_labels=10,
height=0.5,
start=0, end=len(records[org]))
