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Speed up read_airr #367

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grst opened this issue Oct 9, 2022 · 0 comments
Open

Speed up read_airr #367

grst opened this issue Oct 9, 2022 · 0 comments
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scirpy-dev

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grst commented Oct 9, 2022

Description of feature

Loading AIRR data with 1.5M rows takes ~10 minutes. This is not too bad, but could be made less annoying

  • Make validation optional (I expect the validation of the airr implementation takes a good chunk of that time)
  • Parallelization (read different parts of the file in parallel - or first read into pandas, parse several chunks of the dataframe in parallel)
  • Progress bar (this at least shows that this will eventually finish)
@grst grst added this to prio2 in scirpy-dev Oct 9, 2022
@grst grst mentioned this issue Oct 9, 2022
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@grst grst mentioned this issue Mar 29, 2023
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@grst grst moved this from prio2 to ToDo in scirpy-dev Mar 29, 2023
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