Sequence

Reference

SequenceFile

Class for working with fasta genome sequence file.

Usage

For some tasks, such as converting .bedGraph files to Bismark reports, BSXplorer needs information about all cytosines in reference genome. For such tasks the user need to preprocess reference genome with SequenceFile. Afterwards, preprocessed cytosine file can be used in dedicated functions.

import bsxplorer as bsx

file = bsx.SequenceFile("path/to/genomeseq.fa")
file.preprocess_cytosines("path/to/output.parquet")