simple-gtf

Simple GTF reader outputting as a Polars dataframe.

GTF files are notoriously inconsistent so this may not work with all. It has been primarily tested with Ensembl and FlyBase GTF files. This repository is primarily intended for personal use and no guarantees are made about its helpfulness for others.

Installation

pip install git+https://github.com/tgbrooks/simple_gtf
# or, if using uv:
uv add "simple_gtf @ git+https://github.com/tgbrooks/simple_gtf"

Use

import simple_gtf

# Read in a gtf file
gtf = simple_gtf.read_gtf("example.gtf.gz")

# For example, get transcript-gene pairs as a polars dataframe
gtf.select("transcript_id", "gene_id").explode("transcript_id").explode("gene_id").drop_nulls().unique()

# Load in only specific feature types for faster run-time and lower memory
gtf = simple_gtf.read_gtf("example.gtf.gz", features=["gene", "exon"])

Alternatives

gffutils is much more full-featured and persists its parsing into a sqlite file, which makes subsequent access very fast. However, it parses attributes as json entries in the table instead of as separate columns, which makes attributes less convenient.