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lgenome

A python package to manage curated genomic resources for bioinformatics workflows.

Introduction

This library is a lightweight wrapper over AWS S3 that fetches curated "genome resources" under a stable interface and naming system.

For each genome managed by latch, a collection of URLS pointing to well-defined "genome resources" is maintained and represented by the below class:

class GenomeData:
    gtf: str
    ref_genome: str
    ref_trans: Optional[str]
    salmon_index: Optional[str]
    STAR_index: Optional[str]

Genome resources themself, eg. a reference genome, can be retrieved through a standardized interface.

  • def download_gtf(self) -> Path
  • def download_ref_genome(self) -> Path
  • def download_ref_trans(self) -> Path
  • def download_salmon_index(self) -> Path
  • def download_star_index(self) -> Path

There really isn't much else to this.