txview 0.1.1

Plot transcript models for a gene from a GTF in the terminal.

txview

Terminal plotter for transcript models of a gene from a GTF annotation.

Install

Latest from main:

pip install "txview @ git+https://github.com/ymvk/monorepo@main#subdirectory=packages/txview"

Pin to a version tag:

pip install "txview @ git+https://github.com/ymvk/monorepo@txview-v0.1.0#subdirectory=packages/txview"

CLI

txview path/to/annotation.gtf BRCA1

Accepts .gtf or .gtf.gz. The gene may be specified by gene_name or gene_id.

Flags:

Flag	Default	Description
--width	terminal width - 30	Display width in columns
--intron-width	5	Columns reserved per truncated intron

Example

BRCA1 [chr17:43044295-43125483] (-)
ENST00000357654  │████████████████████████████╌╌╌╌╌█╌╌╌╌╌█╌╌╌╌╌█╌╌╌╌╌██╌╌╌╌╌██╌╌╌╌╌██╌╌╌╌╌███████████████████████████◀
ENST00000471181  │████████████████████████████╌╌╌╌╌─╌╌╌╌╌─╌╌╌╌╌─╌╌╌╌╌██╌╌╌╌╌──╌╌╌╌╌──╌╌╌╌╌███████████████████████◀
ENST00000586385                                    │╌╌╌╌╌─╌╌╌╌╌█╌╌╌╌╌──╌╌╌╌╌██╌╌╌╌╌──╌╌╌╌╌█◀

Legend:

Char	Meaning
█	Exon
─	Intron within a transcript's span (e.g. alternative splicing)
╌	Truncated intron region (intergenic-like compression for display)
▶	TSS (5' end) on + strand; ◀ on - strand
│	TTS (3' end)

Python API

from txview import parse_gtf, layout, render

transcripts = parse_gtf("annotation.gtf", "BRCA1")
segments, width = layout(transcripts, total_width=120, intron_width=5)
print(render(transcripts, segments, width))

parse_gtf returns dict[str, Transcript] keyed by transcript_id.