Python work creating BED file - TypeError: expected str, bytes or os.PathLike object, not _io.TextIOWrapper

Question

I have problem with a code. Im trying to create new bed file (The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations) to use it in my school work. I think its fine but it gives me back an error:

    Traceback (most recent call last):
  File "C:\Users\AppData\Local\Programs\Python\Python38\nano.py", line 50, in <module>
    read_bed( simple_repeats_file )
  File "C:\Users\AppData\Local\Programs\Python\Python38\nano.py", line 30, in read_bed
    with(open(file,"r")) as bed:
TypeError: expected str, bytes or os.PathLike object, not _io.TextIOWrapper

and I don´t know what to do with it.

#!/usr/bin/python

import os
import random
import pathlib
pick_random = 100000
mask_regions = dict()

genome = {
    'chr01' : 41767771,
    'chr02' : 34826099,
    'chr03' : 43931233,
    'chr04' : 45086258,
    'chr05' : 46513039,
    'chr06' : 43117521,
    'chr07' : 39373400,
    'chr08' : 51314288,
    'chr09' : 47719527,
    'chr10' : 40511255,
    'chr11' : 34663808
}

genome_length = sum(genome.values())

simple_repeats_file = open("simpleRepeats.bed","w")

gaps_file = open("gap.bed","w")

def read_bed( file ):
    with(open(file,"r")) as bed:
        for line in bed:
            line = line.rstrip()
            chr, start, end = line.split("\t")
            chr = chr.replace('chr','')
            if chr == 'X':
                chr = 23
            try:
                chr = int(chr)
            except:
                continue
            if not chr in genome:
                continue
            if not chr in mask_regions:
                mask_regions[chr] = dict()
            if not start in mask_regions[chr]:
                mask_regions[chr][int(start)] = dict()
            mask_regions[chr][int(start)][int(end)] = 1


read_bed( simple_repeats_file )
read_bed( gaps_file )

random_positions = dict()

while( len(random_positions.keys()) < pick_random ):
    randnum = random.randrange(1,genome_length)
    tmp_length = 0
    for chr, chrlength in sorted(genome.iteritems()):
        if randnum < tmp_length+chrlength:
            randchr = chr
            randpos = randnum-tmp_length
            break
        tmp_length += chrlength
    
    mask = False
    for mask_start in sorted(mask_regions[randchr]):
        if randpos < mask_start:
            break
        for mask_end in sorted(mask_regions[randchr][mask_start]):
            if randpos <= mask_end:
                #print( "MASK" )
                mask = True
                break
    if not mask:
        random_positions["\t".join([str(randchr),str(randpos),str(randpos+1)])] = 1

print( "\n".join(random_positions.keys()) )

I tried to solve it with PathLib library and some other things I found on inte.net, but still nothing.

Answer 1

You open two files right away:

simple_repeats_file = open("simpleRepeats.bed","w")
gaps_file = open("gap.bed","w")

Then you call read_bed on those:

read_bed( simple_repeats_file )
read_bed( gaps_file )

read_bed tries opening the file given to it as an argument:

def read_bed( file ):
    with(open(file,"r")) as bed:
    ...

So what essentially happens is

with open(open("simpleRepeats.bed","w"), "r") as bed:
    ...

This code, of course, crashes.