gtf-pyparser 0.2.1

A lightweight, dependency-free GTF parser returning a structured Gene/Transcript/Interval object model.

gtf_pyparser

A lightweight, dependency-free Python library for parsing GTF (Gene Transfer Format) files into a structured object model.

Why gtf_pyparser?

Most GTF parsing libraries are either too heavy (requiring pandas, SQLite, or large C extensions) or return flat data structures that don't reflect the natural hierarchy of genomic annotation. gtf_pyparser gives you a clean Gene → Transcript → features object model with no dependencies beyond the Python standard library.

Curently working on direct acces indexing by name and position.

Installation

pip install gtf_pyparser

Quick start

import gtf_pyparser

genes = gtf_pyparser.parse_gtf("Homo_sapiens.GRCh38.gtf")

gene = genes["ENSG00000139618"]
print(gene.symbol, gene.start, gene.end)

for transcript_id, transcript in gene.transcript.items():
    exons = transcript.features.get("exon", [])
    introns = gtf.get_intron(exons)
    print(f"  {transcript_id}: {len(exons)} exons, {len(introns)} introns")

Coordinate convention

All coordinates are 0-based half-open (start inclusive, end exclusive), consistent with BED and BAM format. GTF files are 1-based inclusive; the conversion is applied automatically during parsing.

API

Parsing

gtf.parse_gtf(gtf_file, primary_key="gene_id")

Parse a GTF file into a dictionary of Gene objects.

genes = gtf_pyparser.parse_gtf("annotation.gtf")
genes = gtf_pyparser.parse_gtf("annotation.gtf", primary_key="gene_name")

• gtf_file — path to the GTF file
• primary_key — attribute used to key the returned dictionary (default: "gene_id")
• Returns — dict[str, Gene]

gtf.get_attr(string)

Parse a raw GTF attribute string into a key-value dictionary. Useful when processing GTF lines outside of the full parser.

attrs = gtf_pyparser.get_attr('gene_id "ENSG00000139618"; gene_name "BRCA2";')
# {"gene_id": "ENSG00000139618", "gene_name": "BRCA2"}

Derived features

gtf.get_intron(exons)

Derive intron intervals from a list of exon Interval objects belonging to a single transcript. Introns are numbered biologically: from 1 upward on the + strand, and from n down to 1 on the - strand.

exons = transcript.features.get("exon", [])
introns = gtf_pyparser.get_intron(exons)

• exons — list of Interval, need not be pre-sorted
• Returns — list[Interval], empty if fewer than two exons are provided

Data classes

Interval

Immutable genomic coordinate record. All Interval objects are frozen — they are replaced rather than mutated when coordinates need updating.

Attribute	Type	Description
chr	str	Chromosome or sequence name
start	int	0-based start (inclusive)
end	int	0-based end (exclusive)
strand	str	"+", "-", or "." for unstranded
phase	int or str	Reading frame (0, 1, 2), or "." if not applicable
attribute	dict	Key-value pairs from the GTF attribute column

Transcript

Groups all GTF records sharing a transcript_id. The genomic span always reflects the union of all features seen so far.

Attribute	Type	Description
transcript_id	str	Ensembl transcript ID or equivalent
transcript_symbol	str or None	Human-readable transcript symbol
interval	Interval	Current genomic span of the transcript
features	dict[str, list[Interval]]	Feature type → list of intervals

Convenience properties: start, end, phase, attribute.

Gene

A gene locus containing one or more transcript isoforms.

Attribute	Type	Description
gene_id	str	Primary identifier (e.g. Ensembl gene ID)
symbol	str	Gene symbol, resolved from gene_symbol, gene_name, or gene_id
interval	Interval	Genomic span from the GTF gene record
transcript	dict[str, Transcript]	Transcript ID → Transcript

Convenience properties: start, end, phase, attribute, biotype, has_transcript.

Logging

Progress and error messages are emitted under the "gtf_pyparser" logger. To suppress informational output:

import logging
logging.getLogger("gtf_pyparser").setLevel(logging.WARNING)

License

MIT Citation aknowledge : Romain Lannes 2026