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)