Speeding up the python scripts

ParkinsonLab / Metatranscriptome-Workshop

Metatranscriptomics Tutorial

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Speeding up the python scripts #17

Closed eray-sahin closed 3 years ago

eray-sahin commented 3 years ago

Hello,

I am trying to use your pipeline for analysis of another metatranscriptomics data, and now the python script#6 is running. The run time of python script #5 was more than 7 days. As I am not familiar with Python language, I wanted to ask a simple question whether it is possible to speed up.

Thank you,

Best regards,

Eray

billytaj commented 3 years ago

we don't really recommend using this tutorial to run your own data. many coding considerations were made specifically for this singular dataset. we'll be launching a new pipeline, with a new tutorial soon that's much more flexible to people who have their own data to run

Felix-Matheri commented 3 years ago

Dear @billytaj whats the progress with this new pipeline? Looking forward https://github.com/ParkinsonLab/Metatranscriptome-Workshop/issues/17#issuecomment-780060979