add profiling & fix major bottleneck

sjteresi / TE_Density

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4

GNU General Public License v3.0

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add profiling & fix major bottleneck #83

Closed teresi closed 3 years ago

teresi commented 3 years ago

add single process mode to process_genome.py
add profiling with cProfile to density calcs in single process mode
fix bug where reading H5py dataset too often slowed down processing

you can turn on profiling using the --single-process flag it was sped up by moving the read call to one of the datasets out of the inner loop