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How to calculate bowtie2 run time using python

Hello dear one,

I am new to programming! I want to calculate the run duration of bowtie2 and bwa. 1. First I don't know (the program) how to run a bowtie2 in python script! 2. And I want to know how to calculate time using python! Can you please help me?

Thanks in advance!

rna-seq bowtie2 alignment python
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updated by Devon Ryan Devon Ryan • written by John John

Please do not delete posts that have received answers or have been solved. You should accept (green mark) @Devon's answer if it helped solve your question.

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written by GenoMax GenoMax

1 answer

  1. Read the documentation for bowtie2/bwa regarding how to run them.
  2. Do so from the command line.
  3. Once you can do (2), see the python subprocess module.
  4. You can google for python date and timedelta
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written by Devon Ryan Devon Ryan

Thank you Dr. Devon-Ryan, I have learnt how to use bowtie and bwa, since I am new for python I found subprocess module as very tough one! I will learn sooner!

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written by John John

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