grelu.io

grelu.io contains methods for reading and writing data into different file formats. It includes individual submodules for standard genomic formats such as FASTA, BED, and others, as well as miscellaneous functions for other formats.

Submodules

• grelu.io.bed
• grelu.io.bigwig
• grelu.io.fasta
• grelu.io.genome
• grelu.io.motifs

Functions

read_tomtom(→ pandas.DataFrame)	Reads TOMTOM output files into a dataframe
update_ckpt(→ None)	Update legacy model checkpoint files saved with gReLU v0.4 or lower. Creates

Package Contents

grelu.io.read_tomtom(tomtom_dir: str, qthresh: float = 0.05) → pandas.DataFrame

Reads TOMTOM output files into a dataframe

Parameters:

• tomtom_dir – Path to a directory containing TOMTOM output files

• qthresh – q-value threshold. Only TOMTOM hits with q-value lower than this will be returned.

Returns:

A dataFrame containing TOMTOM matches with q-value lower than threshold.

grelu.io.update_ckpt(ckpt_file: str, out_file: str | None = None) → None

Update legacy model checkpoint files saved with gReLU v0.4 or lower. Creates a new checkpoint file which can be loaded using grelu.lightning.LightningModel.load_from_checkpoint

Parameters:

• ckpt_file – Path to a legacy checkpoint file saved with gReLU v0.4 or lower

• out_file – Path to the output file