3 releases
0.1.2 | Jul 19, 2023 |
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0.1.1 | Jul 19, 2023 |
0.1.0 | Jul 19, 2023 |
#10 in #gtf
42KB
gtf2json
A simple CLI utility to convert a GTF file to NDJSON for fast parsing
Summary
The GTF file format is fantastic when working with bedtools
since it is essentially
a modified version of the BED
file format.
However, if you're interested in the annotations column, it can be a massive headache to parse - especially if you're operating on the full genome.
I wrote this tool to convert the GTF file format into streamable newline-delim JSON.
This makes it convenient to load with polars
in python incredibly fast and skip
all the annotation parsing.
Installation
You can install this with the rust package manager cargo
:
cargo install gtf2json
Usage
# classic i/o
gtf2json -i <input.gtf> -o output.json
# write to stdout
gtf2json -i <input.gtf>
Dependencies
~3–4MB
~79K SLoC