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January 3, 2016 06:39
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| """ | |
| Illustrates how to use pybedtools to count motifs along sliding windows | |
| of UTRs from a GFF file. | |
| This uses example data shipped with pybedtools. | |
| """ | |
| import pybedtools | |
| def renamer(f): | |
| # BEDTools sees the featuretype of a GFF file as the "name" when using | |
| # makewindows, so we need to set the featuretype to be the ID. Or whatever | |
| # GFF attribute is of interest. | |
| if f[2] == 'UTR': | |
| f[2] = f['ID'] | |
| return f | |
| # Prepare the UTRs file | |
| utrs = pybedtools.example_bedtool('gdc.gff')\ | |
| .each(renamer) | |
| # 20-bp windows, labeled by their name and an integer | |
| windows = pybedtools.BedTool().window_maker(b=utrs, w=20, i='srcwinnum' ) | |
| motifs = pybedtools.example_bedtool('gdc.bed') | |
| # Count up the number of features in each window. | |
| # Last column of this file will have the number of motifs hitting that window | |
| results = windows.intersect(motifs, c=True) |
My pybedtools is:
pybedtools-0.6.2-py2.7-linux-x86_64.egg
(upgrading to 0.6.4 and BEDTools 2.18 solved this)
BEDTools makewindows doesn't keep strand information, so if you need strand then you need a different strategy:
def stranded_windows(f, n=5):
name = f['ID']
for i, start in enumerate(range(0, len(f) - n, n)):
f.start = start
f.stop = start + n
f.attrs['ID'] = '%s_%s' % (name, i)
yield f
windows = pybedtools.example_bedtool('gdc.gff')\
.filter(lambda x: x[2] == 'UTR')\
.split(stranded_windows)
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If I try this I get: