This package uses Python3 and a number of third party packages. It is recommended to set up and activate a virtualenv to contain the dependencies by running:
virtualenv --python=python3 sctoo-venv
source sctoo-venv/bin/activate
Installation has to be done manually with the setup.py script.
python setup.py build sdist
pip install dist/sctoo-0.1.tar.gz
Example use case 1: Bin all varscan2 annotated somatic variants in data/varscan.somatic.snp.vcf according to the intervals defined by data/gene_intervals.bed and print them to the command line in bed format.
sctoo binner --variants data/varscan.somatic.snp.vcf --intervals data/gene_intervals.bed --only-somatic
Example use case 2: Bin all variants in data/varscan.somatic.snp.vcf according to the intervals defined in data/gene_intervals.bed and write them to the file binned_variants.bed.
sctoo binner --variants data/varscan.somatic.indel.vcf --intervals data/gene_intervals.bed --out binned_variants.bed
No comman line utilities for fitting linear models, yet.