How are paths meant to be denoted on for Biopython on mac?

Question

I am trying to run a basic biopython script to rename sequences within a fasta file. I have only ever ran this on a server; i am trying to do it on my macbook but I can't work out what the correct path to the file should be.

on the server is worked as follows:

original_file = r”/home/ggb_myname/Documents/Viromex/Viromex.contigs.fa”

I am trying to do the same thing on my mac with

original_file = r"/Users/u2188165/Documents/Home/Post-qiime/dna-sequences.fasta" 

and it returns the error

FileNotFoundError: [Errno 2] No such file or directory: '/Users/u2188165/Documents/Home/Post-qiime/dna-sequences.fasta

I know this is probably basic, but I can't find the correct way to write the path, either on my own or online.

Answer 1

Try using libraries like pathlib and os. Makes your code more modular and os independent to use.

from pathlib import Path
import os

dir ="/Users/u2188165/Documents/Home/Post-qiime"
file= "dna-sequences.fasta"

full_path = os.path.join(str(Path(dir)), file)

Or even try drill down approach for more versatility.

from pathlib import Path
import os

path_drill =  ["Users","u2188165","Documents","Home","Post-qiime"]
file= "dna-sequences.fasta"

full_path = str(Path(os.path.join(*path_drill, file)))

How/Where you want to store this is upto your imagination and requirements.

Happy coding!