gtf-polars 0.1.0

Parse GTF files with Polars

gtf-polars

Parse GTF files with Polars

Implements a memory-efficient GTF parser that stays fully lazy until .collect() is called. For more information on Polars Lazy API, see this link

Scripts

scripts/subset_gtf_feature.py

Filters a GTF file to keep only rows matching one or more feature types (e.g. gene, transcript, exon) and writes the result as a tab-separated GTF file.

python scripts/subset_gtf_feature.py gencode.v39.annotation.gtf \
    --feature gene transcript \
    --output subset.gtf

Argument	Description
gtf_file	Path to the input GTF or gzipped GTF file
--feature	One or more feature types to keep
--output	Output path (default: subset.gtf)

---

scripts/transcript_to_gene.py

Builds a transcript-to-gene mapping CSV from a GTF file by extracting transcript_id, gene_id, and gene_name from transcript rows. Useful for downstream tools (e.g. alevin, tximeta) that require a tx2gene table.

python scripts/transcript_to_gene.py isoseq.gtf --output transcript_to_gene.csv

Argument	Description
gtf_file	Path to the input GTF file
--output	Output CSV path (default: transcript_to_gene.csv)

---

Library usage

from gtf_polars import parse_gtf
import polars as pl

lf = parse_gtf("gencode.v39.annotation.sorted.gtf", attributes_to_extract=["gene_id", "gene_name"])

df = (lf.filter(pl.col("feature") == 'transcript').select(['seqname', 'start','end','gene_id', 'gene_name']).collect())

df.head()
shape: (5, 5)
┌─────────┬───────┬───────┬───────────────────┬─────────────┐
│ seqname ┆ start ┆ end   ┆ gene_id           ┆ gene_name   │
│ ---     ┆ ---   ┆ ---   ┆ ---               ┆ ---         │
│ str     ┆ i64   ┆ i64   ┆ str               ┆ str         │
╞═════════╪═══════╪═══════╪═══════════════════╪═════════════╡
│ chr1    ┆ 11869 ┆ 14409 ┆ ENSG00000223972.5 ┆ DDX11L1     │
│ chr1    ┆ 12010 ┆ 13670 ┆ ENSG00000223972.5 ┆ DDX11L1     │
│ chr1    ┆ 14404 ┆ 29570 ┆ ENSG00000227232.5 ┆ WASH7P      │
│ chr1    ┆ 17369 ┆ 17436 ┆ ENSG00000278267.1 ┆ MIR6859-1   │
│ chr1    ┆ 29554 ┆ 31097 ┆ ENSG00000243485.5 ┆ MIR1302-2HG │
└─────────┴───────┴───────┴───────────────────┴─────────────┘