sainsc.io.read_gem_file

sainsc.io.read_gem_file(filepath, *, sep='\t', n_threads=None, **kwargs)

Read a GEM file into a DataFrame.

GEM files are used by e.g. Stereo-Seq and Nova-ST.

The gene-ID and count column will be renamed to gene and count, respectively.

The name of the count column must be one of MIDCounts, MIDCount, or UMICount.

Parameters:

• filepath (PathLike or str) – Path to the GEM file.

• sep (str, optional) – Separator used in polars.read_csv().

• n_threads (int, optional) – Number of threads used for reading and processing file. If None this will default to the number of available CPUs.

• kwargs – Other keyword arguments will be passed to polars.read_csv().

Return type:

polars.DataFrame

Raises:

ValueError – If count column has an unknown name.