Ge.get_final_edit_status

Ge.get_final_edit_status#

missionbio.mosaic.ge.Ge.get_final_edit_status

Ge.get_final_edit_status(edit_mode: str = 'indel') → DataFrame#

Get the final_edit_status DataFrame for the given edit mode. If the data is not already cached, it will be generated.

Parameters:
edit_modestr

The type of edits to consider. Can be one of “indel”, “snv”, or “indel_snv”. Default is “indel”. If “indel_snv”, both SNV and INDEL variants are considered.

Returns:
pd.DataFrame

DataFrame containing the final edit status for the specified edit mode. Contains the targets as columns and the cells as rows. Has the following possible values for each cell/target combination:

  • “WT”: Wild-type genotype

  • “Mono-allelic edit”: Mono-allelic edit

  • “Bi-allelic edit”: Bi-allelic edit

  • “No-call”: Both alleles failed the filters, i.e. no-call.

  • “WT+No-call”: Wild-type genotype with no-call. This happens when 1 of the alleles fails the filters and other has a WT genotype.

  • “Mono+No-call”: Mono-allelic edit with no-call. This happens when 1 of the alleles fails the filters and other has a mono-allelic edit.

Raises:
ValueError

If the edit_mode is not one of “indel”, “snv”, or “indel_snv”.

Ge

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