scallops.reads.peaks_to_bases

scallops.reads.peaks_to_bases(maxed, peaks, labels=None, labels_only=True, bases=('G', 'T', 'A', 'C'))

Convert peaks to bases.

Parameters:

• maxed (DataArray) – Maxed array (sigma,t,c,y,x)

• peaks (DataFrame | DataFrame) – Peaks data frame which has been filtered to retain only peaks of interest. Note that if peaks is a dask data frame, it is loaded into memory using dask.compute.

• labels (ndarray | DataArray | None) – Segmentation array (y,x)

• labels_only (bool) – If true, only return peaks where labels are present.

• bases (Sequence[str] | None) – List of bases.

Returns:

DataArray with dimensions (read,t,c) where read is spot with coordinates y, x, peak, and label

Return type:

DataArray