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)
infile, outfile = sys.argv[1:3]
df = pandas.read_excel(infile, header=2, index_col=0)
tmpfile = pybedtools.BedTool._tmp()
df = df.sort_values(['chrom', 'start', 'end'])
df['epigenetic class'] = df['epigenetic class'].apply(lambda x: x.replace(' ', '_'))
colors = {
'Active': '153,0,0',
'Null': '136,136,136',
'HP1_centromeric': '51,102,0',
'PcG': '0,51,102',
}
df['itemRgb'] = df['epigenetic class'].apply(lambda x: colors[x])
df['strand'] = '.'
df['thickStart'] = df['start']
df['thickEnd'] = df['end']
df['score'] = 0
order = [
'chrom',
'start',
'end',
'epigenetic class',
'score',
'strand',
'thickStart',
'thickEnd',
'itemRgb']
df[order].to_csv(tmpfile, header=False, index=False, sep='\t')
bigbed.bigbed(pybedtools.BedTool(tmpfile), 'dm3', outfile)
#!/usr/bin/env python import pybedtools from pybedtools.contrib.bigbed import bigbed import sys source, dest = sys.argv[1:3] bigbed(pybedtools.BedTool(source).cut([0, 1, 2]).sort(), 'dm3', dest)
