Python wrapper for the bwtool library.
Project description
Python wrapper for the bwtool library. Please take a look to the bwtool wiki for notes on the installation process and to the known issues listed below within this readme.
How do I install this package?
As usual, just download it using pip:
pip install pybwtoolTests Coverage
Since some software handling coverages sometime get slightly different results, here’s three of them:
Extract
The extract method returns a tuple of pandas Dataframes
with the data from the regions of a bed file extracted from the given bigwig.
from pybwtool import extract
bed, scores = extract(
bed_path="path/to/my/bed_file.bed",
bigwig_path="path/to/my/bigwig_file.bigwig",
nan_threshold=0.95 # maximum amount of NaN to allow, otherwise the line is dropped
)The obtained dataframes look as follows:
chrom |
chromStart |
chromEnd |
|---|---|---|
chr11 |
14606206 |
14606406 |
chr1 |
1336296 |
1336496 |
chr11 |
47745644 |
47745844 |
chr11 |
62609072 |
62609272 |
chr14 |
21523971 |
21524171 |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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0.37 |
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0.35 |
0.33 |
0.31 |
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0.29 |
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0.28 |
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1.25 |
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1.32 |
1.43 |
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1.36 |
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1.32 |
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1.43 |
1.5 |
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1.64 |
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1.71 |
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1.58 |
1.56 |
1.43 |
1.36 |
1.24 |
1.24 |
1.28 |
1.26 |
1.33 |
1.36 |
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1.46 |
1.43 |
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1.42 |
1.39 |
1.37 |
1.37 |
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1.43 |
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1.42 |
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1.44 |
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1.37 |
1.36 |
1.32 |
1.29 |
1.31 |
1.29 |
1.29 |
1.19 |
1.24 |
1.19 |
1.19 |
1.25 |
1.24 |
1.26 |
1.28 |
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1.37 |
1.33 |
1.33 |
1.28 |
1.24 |
1.25 |
1.25 |
1.25 |
1.26 |
1.24 |
1.22 |
1.28 |
1.28 |
1.32 |
1.37 |
1.39 |
1.36 |
1.32 |
1.31 |
1.36 |
1.33 |
1.5 |
1.5 |
1.5 |
1.5 |
1.5 |
1.47 |
1.46 |
1.49 |
1.57 |
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1.62 |
1.64 |
1.64 |
1.67 |
1.67 |
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1.74 |
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1.72 |
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1.71 |
1.72 |
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1.81 |
1.82 |
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1.71 |
1.67 |
1.68 |
1.65 |
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1.65 |
1.67 |
1.69 |
1.75 |
1.64 |
1.57 |
1.44 |
1.6 |
1.69 |
1.68 |
1.72 |
1.69 |
1.71 |
1.67 |
1.64 |
1.49 |
1.46 |
0.04 |
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0.04 |
0.04 |
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0.04 |
0.04 |
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nan |
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0.01 |
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0.01 |
nan |
nan |
nan |
nan |
nan |
nan |
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nan |
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0.01 |
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0.01 |
0.01 |
0.01 |
0.01 |
0.03 |
0.03 |
0.03 |
0.03 |
0.03 |
0.01 |
0.31 |
0.25 |
0.21 |
0.19 |
0.19 |
0.19 |
0.19 |
0.18 |
0.19 |
0.21 |
0.21 |
0.21 |
0.21 |
0.22 |
0.26 |
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0.26 |
0.26 |
0.29 |
0.28 |
0.26 |
0.26 |
0.26 |
0.26 |
0.28 |
0.26 |
0.24 |
0.24 |
0.22 |
0.24 |
0.25 |
0.25 |
0.25 |
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0.29 |
0.28 |
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0.29 |
0.29 |
0.25 |
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0.26 |
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0.28 |
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0.26 |
0.26 |
0.26 |
0.26 |
0.25 |
0.24 |
0.19 |
0.19 |
0.19 |
0.19 |
0.17 |
0.17 |
0.17 |
0.17 |
0.17 |
0.15 |
0.14 |
0.15 |
0.15 |
0.15 |
0.18 |
0.17 |
0.15 |
0.15 |
0.15 |
0.12 |
0.11 |
0.12 |
0.14 |
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0.15 |
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0.15 |
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0.14 |
0.14 |
0.14 |
0.14 |
0.12 |
0.12 |
0.11 |
0.11 |
0.1 |
0.1 |
0.1 |
0.1 |
0.1 |
0.1 |
0.12 |
0.12 |
0.12 |
0.12 |
0.11 |
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0.12 |
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0.14 |
0.12 |
0.14 |
0.15 |
0.15 |
0.15 |
0.15 |
0.17 |
0.17 |
0.17 |
0.17 |
Common fixes for getting bwtool to work
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