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Help with Python script

Dear all, I am trying to use a program called phyphy. This program runs into python. I would like to create a script that can run in all my files. i. e., in the line e = Extractor("/path/to/FEL.json") the program uses a file in .json format but I have thousands of .json files. So, I want to create a script that can run for all the files that I have stored in several folders.

This is how I run the program into python but this is just for one file. 

import phyphy

### Define a FEL Extractor, for example
e = Extractor("/path/to/FEL.json") 
e.extract_csv("fel.csv")  ## save to fel.csv

### tab-delimited output, as fel.tsv
e.extract_csv("fel.tsv", delim = "\t")
python script
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updated by GenoMax GenoMax • written by imda • imda

Please format your code using the code formatting button: enter image description here

Additionally, it's not clear what you have tried or what in particular you're having trouble with. Looping through files or running a script on many files is fairly straightforward, and there are many, many tutorials on how to do so that can be found with minimal searching.

• 0 views • link
written by jared.andrews07 jared.andrews07

1 answer 

   import glob
   files=[]
   for folder in list-of-folders:
      fnames=glob.glob(f'{folder}/*.json')
      files+=fnames

   for f in files:
      your-scripts
• 0 views • link
written by shoujun.gu shoujun.gu

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