BEDTools style repository for passing VCF/BED files.
Designed to combined variant calls from peaked data with the reference genome. Returns the genomic sequence of the allele most present in the peak.
Example Usage:
import eds_tools
py_eds_tool = eds_tools.EdsTool("/<path>/analysis_regions.txt")
py_eds_tool = py_eds_tool.sequence(
fi= "/<path>/genome.fa",
vcf="/<path>/gatk-snp-indel.vcf.gz"
)
sequences = py_eds_tool.sequences
To run the unittests please run:
cd eds_tools
python -m unittest discover