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]))