def test_color_conversions(self):
"""Test color translations."""
translator = ColorTranslator()
# Does the translate method correctly convert the passed argument?
self.assertEqual(
translator.float1_color((0.5, 0.5, 0.5)),
translator.translate((0.5, 0.5, 0.5)),
"Did not correctly translate colour from floating point RGB tuple",
)
self.assertEqual(
translator.int255_color((1, 75, 240)),
translator.translate((1, 75, 240)),
"Did not correctly translate colour from integer RGB tuple",
)
self.assertEqual(
translator.artemis_color(7),
translator.translate(7),
"Did not correctly translate colour from Artemis colour scheme",
)
self.assertEqual(
translator.scheme_color(2),
translator.translate(2),
"Did not correctly translate colour from user-defined colour scheme",
)
def test_color_conversions(self):
"""Test color translations."""
translator = ColorTranslator()
# Does the translate method correctly convert the passed argument?
assert translator.float1_color((0.5, 0.5, 0.5)) == translator.translate((0.5, 0.5, 0.5)), \
"Did not correctly translate colour from floating point RGB tuple"
assert translator.int255_color((1, 75, 240)) == translator.translate((1, 75, 240)), \
"Did not correctly translate colour from integer RGB tuple"
assert translator.artemis_color(7) == translator.translate(7), \
"Did not correctly translate colour from Artemis colour scheme"
assert translator.scheme_color(2) == translator.translate(2), \
"Did not correctly translate colour from user-defined colour scheme"
def draw_by_bio(info, cates, long_intervals, seqlen, filename):
import diagram as _dia
reload(_dia)
diagram = _dia.Diagram('Test Diagram')
inner_colors, outer_colors = read_colors()
if len(cates) > len(outer_colors):
raise Exception('outer_colors num: %s, cannot satisfy category num: %s' % (len(outer_colors), len(cates)))
color_map = zip(cates, outer_colors)
color_trans = ColorTranslator()
color_name_pairs = [(color_trans.translate(t[1]), t[0]) for t in color_map]
color_map = dict(color_map)
def _add_feats(feature_set, i, width=3, minimal_angle_margin=20):
loc, concur_cates = info[i]
concur_cates = concur_cates.keys()
concur_num = len(concur_cates)
# -------- calc width --------
prev = 0
if i > 0:
prev = info[i - 1][0]
next = seqlen
if i < len(info) - 1:
next = info[i + 1][0]
width = min((next - prev) / concur_num, width)
if width < 1:
raise Exception('too narrow')
# -------- add feature --------
if concur_num > 1:
angle_sum = (concur_num - 1) * minimal_angle_margin
assert angle_sum < 180
angle_slice = angle_sum / (concur_num - 1)
def _add_feat(cate_i):
color = color_map[concur_cates[cate_i]]
start = loc # - (cate_i - concur_num / 2) * width
end = start + width
feat = SeqFeature(FeatureLocation(start, end, strand=1))
titled_angle = 0
if concur_num > 1:
titled_angle = cate_i * angle_slice - angle_sum / 2
feature_set.add_feature(feat, color=color, tilted_angle=titled_angle)
[_add_feat(cate_i) for cate_i in xrange(concur_num)]
def _add_intervals(feature_set, i):
start, end = long_intervals[i]
feat = SeqFeature(FeatureLocation(start, end, strand=-1))
color = inner_colors[i % len(inner_colors)]
feature_set.add_feature(feat, color=color)
def _add(track):
feature_set = track.new_set()
[_add_feats(feature_set, i, 1) for i in xrange(len(info))]
if long_intervals is not None:
[_add_intervals(feature_set, i) for i in xrange(len(long_intervals))]
def _track(track_level):
track = diagram.new_track(track_level, greytrack=False)
_add(track)
_track(1)
diagram.draw(format='circular', circular=True, pagesize=(8 * cm, 8 * cm), fragments=1, orientation='portrait',
start=0, end=seqlen, circle_core=.7, inner_circle_core=1, color_name_pairs=color_name_pairs)
diagram.write("%s.svg" % filename, "svg")
text = u'输出为%s.svg' % filename
print text.encode(codec)
pagesize = pagesizes.A4
height, width = pagesize
if len(args) == 0:
print("Found nothing to draw")
sys.exit()
d = Drawing(width, height)
margin = 0.5 * inch
metadatanames = {}
namecolours = {}
colour_dict = []
my_tracks = {}
#create translator object for translating artemis colours to GenomeDiagram colours
translator = ColorTranslator()
track_count = 0
tree_positions = []
track_names = {}
input_order = []
for arg in args[::-1]:
if arg.lower() in ["tree", "list"]:
input_order.append(arg.lower())
continue
if arg.split('.')[-1].lower() in [
"plot", "hist", "heat", "bar", "line", "graph", "area", "embl",
"gb", "tab", "bam", "fas", "fasta", "mfa", "dna", "fst",
"phylip", "phy", "nexus", "nxs"
]:
