def test_colorspiral(self):
""" Set of 625 colours, with jitter, using get_colors()."""
boxedge = 20
boxes_per_row = 25
rows = 0
for i, c in enumerate(get_colors(625)):
self.c.setFillColor(c)
x1 = boxedge * (i % boxes_per_row)
y1 = rows * boxedge
self.c.rect(x1, y1, boxedge, boxedge, fill=1, stroke=0)
if not (i + 1) % boxes_per_row:
rows += 1
self.finish()
def test_colorspiral(self):
""" Set of 625 colours, with jitter, using get_colors()."""
boxedge = 20
boxes_per_row = 25
rows = 0
for i, c in enumerate(get_colors(625)):
self.c.setFillColor(c)
x1 = boxedge * (i % boxes_per_row)
y1 = rows * boxedge
self.c.rect(x1, y1, boxedge, boxedge, fill=1, stroke=0)
if not (i+1) % boxes_per_row:
rows += 1
self.finish()
# Convenience function for getting feature locations
def get_ft_loc(org, ft):
for f in records[org].features:
if f.type == "CDS" and f.qualifiers["locus_tag"][0] == str(ft):
return f.location.nofuzzy_start, f.location.nofuzzy_end
# Get data for crosslinks from i-ADHoRe results
data = IadhoreData(
os.path.join("dickeya_all_output_params2", "multiplicons.txt"),
os.path.join("dickeya_all_output_params2", "segments.txt"),
)
full_leaves = data.get_multiplicons_at_level(29)
region_colours = list(get_colors(len(full_leaves), a=5, b=0.33, jitter=0.25))
for midx, m in enumerate(full_leaves):
segments = data.get_multiplicon_segments(m)
# Loop over the pairs of consecutive genomes in the table, and add
# crosslinks for multiplicons
print "Cross-linking multiplicon %d" % m
for idx in range(1, len(orgs)):
org1, org2 = orgs[idx - 1], orgs[idx]
org1loc = list(chain.from_iterable([get_ft_loc(org1, f) for f in segments[org1]]))
org2loc = list(chain.from_iterable([get_ft_loc(org2, f) for f in segments[org2]]))
org1ft = (tracks[org1], min(org1loc), max(org1loc))
org2ft = (tracks[org2], min(org2loc), max(org2loc))
# Need to create a colour rather than pass a tuple - unlike features.
# Raise this bug in Biopython!
c = colors.Color(region_colours[midx][0], region_colours[midx][1], region_colours[midx][2])
crosslink = gd.CrossLink(org1ft, org2ft, c)
regionsets[org] = tracks[org].new_set(name="collinear regions")
# Convenience function for getting feature locations
def get_ft_loc(org, ft):
for f in records[org].features:
if f.type == 'CDS' and f.qualifiers['locus_tag'][0] == str(ft):
return f.location.nofuzzy_start, f.location.nofuzzy_end
# Get data for crosslinks from i-ADHoRe results
data = IadhoreData(os.path.join('dickeya_all_output_params2',
'multiplicons.txt'),
os.path.join('dickeya_all_output_params2',
'segments.txt'))
full_leaves = data.get_multiplicons_at_level(29)
region_colours = list(get_colors(len(full_leaves), a=5, b=0.33,
jitter=0.25))
for midx, m in enumerate(full_leaves):
segments = data.get_multiplicon_segments(m)
# Loop over the pairs of consecutive genomes in the table, and add
# crosslinks for multiplicons
print "Cross-linking multiplicon %d" % m
for idx in range(1, len(orgs)):
org1, org2 = orgs[idx-1], orgs[idx]
org1loc = list(chain.from_iterable([get_ft_loc(org1, f) for f in
segments[org1]]))
org2loc = list(chain.from_iterable([get_ft_loc(org2, f) for f in
segments[org2]]))
org1ft = (tracks[org1], min(org1loc), max(org1loc))
org2ft = (tracks[org2], min(org2loc), max(org2loc))
# Need to create a colour rather than pass a tuple - unlike features.
# Raise this bug in Biopython!
