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abdenlab / oxbow

Read specialized NGS formats as data frames in R, Python, and more.
https://lifeinbytes.substack.com/p/breaking-out-of-bioinformatic-data-silos
Apache License 2.0
59 stars 8 forks source link

Create GFF and GTF readers #41

Closed GarrettNg closed 1 year ago

GarrettNg commented 1 year ago

GFF and GFF Readers

GFF

Doesn't pull out metadata directives or handle tabix indexing.

Usage

import oxbow as ox
import polars as pl

ipc = ox.read_gff("../fixtures/example.gff")
df = pl.read_ipc(ipc)
df

image

GTF

Usage

ipc = ox.read_gtf("../fixtures/example.gtf")
df = pl.read_ipc(ipc)
df

image

Note that score, phase, and frame values parsed as None by Noodles will be null and not ".". phase and frame are a little odd since they are represented as strings with expected values of "0", "1", or "2" and Noodles implements them differently internally.