Speedup CB loading via indexing - #43
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- much faster to access barcode indexes than search via matching - some code optimization: - read file via for loop - access df column directly
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Hello,
Cell barcode loading was quite slow for me (~48 min for a file with 8000 barcodes) and I figured it was because accessing pandas data frame via column matching is quite slow. The implementation via indexing of the df speeds this up dramatically (less than 5 seconds for the same file for me), while producing the exact same dictionary (CB_dict, tested on two different files via md5).
I understand that this may not be a problem on all systems and definitely is not an issue on smaller dataset but maybe it helps others as well.
Cheers,
Philipp