toks[6],
toks[7],
toks[8],
'.',
toks[-1],
'.',
toks[7],
toks[8],
'0,0,0',
]
)
yield contact
bt = pybedtools.BedTool(get_contacts()).saveas()
if len(bt) == 0:
bt = pybedtools.BedTool('chr5_random 92416 92417 . 0 . 92416 92417 0,0,0', from_string=True)
else:
norm = bt.colormap_normalize(vmin=7.0, vmax=18.0)
bt = pybedtools.BedTool(itertools.chain(bt, [get_bait()])).saveas()
cmap = utils.singlecolormap('k')
def recolor(f):
if f.name == '.':
f = featurefuncs.add_color(f, cmap, norm)
f.score = '0'
return f
bt = bt.each(recolor).sort()
bigbed(bt, genome='mm9', output=target)
# Raw data are in GFF-like format. Convert them, add leading "chr" to chrom
# names, and retain score in both score field as well as name field.
def fix(x):
x = featurefuncs.gff2bed(x, name_field=5)
x[4] = x.name
x.chrom = 'chr' + x.chrom
return x
x = pybedtools.BedTool(source)\
.each(fix)\
.saveas()
# Normalize the colormap based on the scores.
norm = x.colormap_normalize()
color = '#000000'
cm = singlecolormap(color)
# Since we've constructed a separate colormap, we disable the score by setting
# to '0'. Keep the names as scores though so we can check in the browser.
def zero_score(f):
f.name = '%.4f' % float(f.score)
f.score = '0'
return f
x = x.each(featurefuncs.add_color, cm, norm)\
.each(zero_score)\
.sort()
bigbed(x.fn, 'dm2', target)
