How to import data from a bed file into GenomeIntervalTree.from_bed
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Entering edit mode
21 months ago
Manuel ▴ 40

I need to import the data of one bed file into GenomeIntervalTree.from_bed().

Looking the code, there are some examples

 test_url = 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadDnd41Ezh239875UniPk.narrowPeak.gz'
 data = zlib.decompress(urlopen(test_url).read(), 16+zlib.MAX_WBITS)
 gtree = GenomeIntervalTree.from_bed(BytesIO(data))

But in this example, data is taken from a url then decompressed, read and them imported. I have been working around to do the same but having the bed file in my computer. How can I do this?

Thanks!

EDIT

And then, following their example, the search method seems no work to me

Example::

gtree[b'chr10'].search(22610878) 


Traceback (most recent call last):
  File "C:\Users\User\Desktop\myeloid-coverage-script\myeloid_transfer.py", line 49, in <module>
    roi_data = roi2(file_path, bedregions)
  File "C:\Users\User\Desktop\myeloid-coverage-script\bin\Coverage2.py", line 71, in roi2
    gtree[b'chr10'].search(22610878)
AttributeError: 'IntervalTree' object has no attribute 'search'

code taken from https://github.com/konstantint/intervaltree-bio/blob/master/intervaltree_bio/__init__.py

GenomeIntervalTree • 355 views
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