Help with Python script
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2.1 years ago
imda ▴ 10

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 • 431 views
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1
Entering edit mode

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.

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Entering edit mode
2.1 years ago
shoujun.gu ▴ 360
   import glob
   files=[]
   for folder in list-of-folders:
      fnames=glob.glob(f'{folder}/*.json')
      files+=fnames

   for f in files:
      your-scripts
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