Bearclaw
Components to help extract features from variants, to be used as part of a pipeline.
Installation
pip3 install bearclaw
Usage
from bearclaw.preprocessing import VariantDataGenerator
from bearclaw.transforms import spectrum
# Dataframe containing locations of VCF files and labels.
dataframe = DataFrame({
"vcf": [
"src/test/resources/GRCh37/sample1.vcf",
"src/test/resources/GRCh37/sample2.vcf",
],
"class": [1, 0],
})
# Transform VCF files into features using `spectrum`, which counts the number of variants by flanking context.
dg = VariantDataGenerator(transform=spectrum)
# Convert dataframe to label `y` and features `X_spectrum` using `spectrum`.
X_spectrum, y = dg.flow_from_dataframe(dataframe, x_col="vcf")
Reference documentation
https://hylkedonker.gitlab.io/bearclaw/
License
The code in this repository is licensed under the MIT License.
1 maintainer
Metadata
1 maintainer
Release files for bearclaw 0.0.4
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