Speed up spot reading #302
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axbazin
reviewed
Nov 25, 2024
ppanggolin/formats/readBinaries.py
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| :param pangenome: Pangenome object without spot | ||
| :param h5f: Pangenome HDF5 file with spot computed | ||
| :param disable_bar: Disable the progress bar | ||
| Args: |
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When reading large pangenome with numerous spots, PPanGGOLiN took a long time to read spots.
This was due to the fact that for each line all families in the spot where associated to the spot, even if they were already associated.
This issue was fixed here.
Benchmark:
Dataset of 3083 E.Coli genomes, with 2036 spots.
Before: read spots 25 minutes, total time 36 minutes
Now: read spots 3.5 seconds, total time 9 minutes 38sec