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Home Page: https://dbretina.github.io/DBRetina/
License: MIT License
DBRetina python package
Home Page: https://dbretina.github.io/DBRetina/
License: MIT License
(and do you mean pleiotropy?)
Prioritizing #4 will probably solve this. And also make it easier to make a conda package.
see: https://pypi.org/project/DBRetina/ => blank project description.
SWIG is painful; consider pybind11 instead.
Associations file = sample: variant
A pseudo-code for the future:
def vcf_to_assoc(vcf_filename, assoc_filename):
# Open the VCF file using a suitable library (e.g., pysam)
vcf_file = open_vcf_file(vcf_filename)
# Open the output file in write mode
with open(assoc_filename, 'w') as assoc_file:
# Loop over each record in the VCF file
for record in vcf_file:
# For each sample in this record
for sample in record.samples:
# Check if this sample has a variant at this position (i.e., genotype is not (0, 0))
if sample_has_variant(sample):
# Prepare a line with sample ID and variant details
line = format_line(sample, record)
# Write this line to the association file
assoc_file.write(line)
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