Read multiple VCF files through PyVCF
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0
Entering edit mode
4 months ago

I am trying this code to read multiple vcf files present in 2 different folders:

import os
import pandas as pd
import vcf

# Folder Path
path1 = "C://Users//USER//Desktop//Anas/VCFs_1/"
path2 = "C://Users//USER//Desktop//Anas/VCFs_2/"
#os.chdir(path1)


def read(f1,f2):
    reader = vcf.Reader(open(f1,f2))
    df = pd.DataFrame([vars(r) for r in reader])
    out = df.merge(pd.DataFrame(df.INFO.tolist()),
                   left_index=True, right_index=True)
    return out
# Read text File


def read_text_file(file_path1,file_path2):
    with open(file_path1, 'r') as f:
        with open(file_path2,'r') as f:
            print(read(path1,path2))


# iterate through all file
for file in os.listdir():
    # Check whether the file is in text format or not
    if file.endswith(".vcf"):
        file_path1 = f"{path1}\{file}"
        file_path2 = f"{path2}\{file}"
        print(file_path1,"\n\n",file_path2)

But it's giving me a permission error? I have also tried to execute code with admin privileges but nothing happened. There is something wrong with the code.

Can anyone fix it?

bioinformatics python • 360 views
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Entering edit mode
4 months ago
liorglic ▴ 870

There are a few strange things with your code, although I'm not sure if any of them should cause a permission error...

  • os.listdir() takes at least one argument - the directory to be listed.
  • for file in os.listdir... - file is a reserved word in python. Don't use it as a variable name.
  • open(f1,f2) - as far as I know open() can't take two files like that.
  • I don't see the functions being called anywhere...

Is this the actual code you are running?

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0
Entering edit mode

It's not actual code.I am trying to modify other code so It could be able to read multiple vcf files present in 2 different folders. Please help to correct it

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0
Entering edit mode

can anyone help me to correct this code?

I am trying this now:

# Import Module
import os
import vcf
# Folder Path
path1 = "C://Users//USER//Desktop//isiah/VCFs_1/"
path2 = "C://Users//USER//Desktop//isiah/VCFs_2/"

def read(f1,f2):
    reader1 = vcf.Reader(open(f1))
    reader2 = vcf.Reader(open(f2))
    df1 = pd.DataFrame([vars(r) for r in reader1])
    out1 = df1.merge(pd.DataFrame(df1.INFO.tolist()),
                   left_index=True, right_index=True)
    df2 = pd.DataFrame([vars(r) for r in reader2])
    out2 = df2.merge(pd.DataFrame(df2.INFO.tolist()),
                   left_index=True, right_index=True)
    return out1,out2

read(path1,path2)

but still i am getting permission error?

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