Error when trying to create a list of files

Question

I have a folder that contains 20 csv files. Each file has about 10 columns and thousands of rows. The csv files look something like the following:

gene	p-value	xyz
acan	0.05	123
mmp2	0.02	456
mmp9	0.07	789
nnos	0.09	123
gfap	0.01	456

I have written the following script with the purpose of going through each file and filtering the rows only by the genes of interest that I have indicated (in this case mmp2 and mmp9).

# the goal is to edit and save the csv files so they only contain the genes of interest

path = '/Users/adriana/Library/Documents/raw_data',
all_files = glob.glob(os.path.join(path, "*.csv")) #make list of file paths 
genes = ["mmp2", "mmp9"]
for file in all_files:
    path = '/Users/adriana/Library/Documents/raw_data'
    df = pd.read_csv(file,delimiter ='t')
    cleaned = df[df['gene'].isin(genes)]
    cleaned.to_csv(file)

However, I get the following error related to creation of the object "all_files":

TypeError: expected str, bytes or os.PathLike object, not tuple

I’ve used this script before seamlessly, so I am not sure what is going on.

Asked By: Adriana

||

Source

Answer 1

try this:

import os
import glob
import pandas as pd



path = '/Users/adriana/Library/Documents/raw_data'  # Removed comma here
all_files = glob.glob(os.path.join(path, "*.csv"))  # make list of file paths 
genes = ["mmp2", "mmp9"]
for file in all_files:
    df = pd.read_csv(file, delimiter='t')
    cleaned = df[df['gene'].isin(genes)]  
    cleaned.to_csv(file, index=False)

Answered By: Aymen Azoui

Error when trying to create a list of files

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