eugene.interpret.filters_to_meme_sdata

eugene.interpret.filters_to_meme_sdata(sdata, filters_var, filter_inds=None, axis_order=('_num_kernels', '_ohe', '_kernel_size'), output_dir=None, filename='filters.meme', alphabet='ACGT', bg={'A': 0.25, 'C': 0.25, 'G': 0.25, 'T': 0.25})

Convert position frequency matrices (PFMs) to a MEME motif file.

Parameters:

• sdata (xr.Dataset) – The dataset containing the PFMs.

• filters_var (str) – The name of the variable containing the PFMs.

• filter_inds (List[int], optional) – The indices of the filters to convert to a MEME file. If not specified, all filters will be converted.

• axis_order (Tuple[str, str, str], optional) – The order of the axes in the PFMs. By default, the axes are assumed to be in the order (num_kernels, ohe, kernel_size).

• output_dir (str, optional) – The directory to write the MEME file to. By default, the MEME file will be written to the output directory specified in the settings.

• filename (str, optional) – The name of the MEME file to write.

• alphabet (str, optional) – The alphabet to use for the MEME file.

• bg (Dict[str, float], optional) – The background frequencies to use for the MEME file.

Return type:

None