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afrendeiro avatar afrendeiro commented on May 24, 2024

This seems specific to the bedtools version (regardless of pybedtools).

The permanent fix should be to update the codebase to the latest bedtools version.
The reason for using an older version is that from 2.24 on, the position of a and b arguments has been swapped in at least one tool. I have to go through, see which ones and update all functions that call the respective pybedtools operation.

Here's how to reproduce the issue with bedtools 2.20.1:

import pandas as pd
import pybedtools

a = pd.DataFrame([
    ['chr1', 9844, 10460],
    ['chr1', 180534, 181797]])


b = pd.DataFrame([
    ['chr1', 10000, 10800, '9_Het'],
    ['chr1', 10800, 16000, '15_Quies'],
    ['chr1', 16000, 16200, '1_TssA'],
    ['chr1', 16200, 19000, '5_TxWk'],
    ['chr1', 19000, 96080, '15_Quies'],
    ['chr1', 96276, 96476, '15_Quies'],
    ['chr1', 97276, 177200, '15_Quies']])


a_ = pybedtools.BedTool.from_dataframe(a)
b_ = pybedtools.BedTool.from_dataframe(b)

res = a_.intersect(b_, wa=True, wb=True, loj=True)
res.to_dataframe()

from toolkit.

afrendeiro avatar afrendeiro commented on May 24, 2024

Fix in 1294ed3

from toolkit.

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