grelu.io

General functions for reading and writing data

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