seqdata.from_region_files

seqdata.from_region_files(*readers, path, fixed_length, bed, max_jitter=0, sequence_dim=None, length_dim=None, splice=False, overwrite=False)

Save a SeqData to disk and open it (without loading it into memory).

Parameters:

• path (str, Path) – Path to save this SeqData to.

• fixed_length (int, bool, optional) –

  int: use regions of this length centered around those in the BED file.

  True: assume the all sequences have the same length and will try to infer it from the data.

  False: write variable length sequences

• bed (str, Path, pd.DataFrame, optional) – BED file or DataFrame matching the BED3+ specification describing what regions to write.

• max_jitter (int, optional) – How much jitter to allow for the SeqData object by writing additional flanking sequences, by default 0

• sequence_dim (str, optional) – Name of sequence dimension. Defaults to “_sequence”.

• length_dim (str, optional) – Name of length dimension. Defaults to “_length”.

• splice (bool, optional) – Whether to splice together regions that have the same name in the BED file, by default False

• overwrite (bool, optional) – Whether to overwrite existing arrays of the SeqData at path, by default False

Return type:

xr.Dataset