episcanpy.api.ct.bld_mtx_fly

episcanpy.api.ct.bld_mtx_fly(tsv_file, annotation, csv_file=None, genome=None, save=False)

Building count matrix on the fly. Expected running time for 10k cells X 100k features on a personal computer ~65min Does not count pcr duplicate. A tbi file with the same filename as the provided tsv_file must be present in the same directory as the tsv file Note that this function is not available on the Windows operating system.

Parameters

tsv_file : name of the file containing the multiplexed reads (tsv or tsv.gz)

annotation : loaded set of features to create the feature matrix from

csv_file : default is None -

genome : default is None - specify if you want to extract a specific genome assembly

save : default is False - supply a file path as str to save generated AnnData object

Output

------

object (also saved as h5ad if save argument is specified) : AnnData