gtfparse
Parsing library for extracting data frames of genomic features from GTF files
Decision gist · record as of 2026-08-14
Yes. gtfparse is a focused, actively maintained tool for a specific bioinformatics task with low install friction and no security vulnerabilities. It is well-suited for anyone working with GTF files in Python, especially in genomics pipelines. The permissive Apache license and support for current Python versions make it a safe choice.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.9 or later.
- Low install friction; pure Python wheel with three common data-processing dependencies (polars, pyarrow, pandas).
- Actively maintained with recent release and steady commit history.
License · maintenance · safety
permissive license (permissive) — Licensed under Apache Software License (permissive), imposing no significant restrictions on use or redistribution.
last release 2026-07-08 (37 days) · last repo commit 2026-07-08 · 129 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 74,339 downloads/mo, #14,849 on PyPI
Alternatives
Verify before relying
pip install gtfparse
from gtfparse import read_gtf
df = read_gtf("gene_annotations.gtf")
df_genes = df[df["feature"] == "gene"]- Whether the package handles malformed or non-standard GTF files gracefully.
- Performance characteristics when parsing very large GTF files (millions of rows).
- Whether StringTie-specific attributes beyond FPKM are reliably parsed.
What it is and what it does
gtfparse is a lightweight parser for GTF files, the standard format for storing genomic feature annotations (genes, transcripts, exons, etc.) with their genomic coordinates and metadata. It reads GTF files directly into pandas, polars, or pyarrow DataFrames, automatically extracting the fixed columns (feature type, sequence name, start, end, strand) and any optional attributes defined in the file's ninth column. The library is designed for bioinformaticians who need to filter, analyze, or combine genomic annotations programmatically.
The package depends on pandas, polars, and pyarrow for data handling, and supports Python 3.9 through 3.12. It has been actively maintained since 2015, with a recent release and steady development. The examples in its documentation show typical workflows: filtering features by type or chromosome, and extracting expression values (like FPKM from StringTie output) into Python dictionaries for downstream analysis.
Use it for
- Filter GTF annotations by feature type (gene, transcript, exon) and genomic location for targeted analysis.
- Extract gene expression values (FPKM, TPM) from StringTie or similar GTF output into a structured format.
- Combine or compare annotations from multiple GTF files by loading them into DataFrames and performing joins.
- Convert GTF attribute columns into typed Python objects using custom column converters for downstream computation.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes.
gtfparse is a focused, actively maintained tool for a specific bioinformatics task with low install friction and no security vulnerabilities. It is well-suited for anyone working with GTF files in Python, especially in genomics pipelines. The permissive Apache license and support for current Python versions make it a safe choice.
Install
gtfparse on PyPI
Before you install
Low install friction; pure Python wheel with three common data-processing dependencies (polars, pyarrow, pandas). Actively maintained with recent release and steady commit history.
Requires Python 3.9 or later.
License in practice
Licensed under Apache Software License (permissive), imposing no significant restrictions on use or redistribution.
Quickstart
pip install gtfparse
from gtfparse import read_gtf
df = read_gtf("gene_annotations.gtf")
df_genes = df[df["feature"] == "gene"]Verify before relying
- Whether the package handles malformed or non-standard GTF files gracefully.
- Performance characteristics when parsing very large GTF files (millions of rows).
- Whether StringTie-specific attributes beyond FPKM are reliably parsed.
Package facts
| License | permissive license permissive |
| Python support | Supports the current Python release >=3.9 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 3 packagespolarspyarrowpandas |
| Maintenance | Actively maintained 37 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 74,339 / month, #14,849 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaEnvironment :: ConsoleIntended Audience :: Science/ResearchLicense :: OSI Approved :: Apache Software LicenseOperating System :: OS IndependentProgramming Language :: PythonProgramming Language :: Python :: 3Programming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.9Topic :: Scientific/Engineering :: Bio-Informatics |
Evidence: gtfparse-2.8.0-py3-none-any.whl
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