Bam file processing function code with parseargs in Python and Ubuntu

Question

I am trying to adapt a piece of code to extract information for specific elements in bam files.

Here is what I have so far:

import pysam
import pandas as pd
import argparse

args = []

def parseargs(required_args=True):
    class formatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawTextHelpFormatter):
     pass

    epilog = ("")
    parser = argparse.ArgumentParser(description='Run.',
                                     epilog=epilog,
                                     formatter_class=formatter)
    readable = argparse.FileType('r')

    parser.add_argument('--bamfile')
    parser.add_argument('--bed_file')
    parser.add_argument('--genome_sizes')
    parser.add_argument('--output')

    global args

    args = parser.parse_args()
    for name, val in vars(args).items():
        if hasattr(val, 'name'):
            setattr(args, name, val.name)
    print(args)
    return args

print(args)

bamfile = "/mnt/d/Axiotl/ABC/Input/bam/ENCFF070PWH.bam"
bed_file = "/mnt/d/R/abc_3a_scaffold_hg19.bed"
output = "/mnt/d/Axiotl/ABC/Output/bam" 
genome_sizes = "/mnt/d/Axiotl/ABC/Working_Copy/ABC-Enhancer-Gene-Prediction-master/reference/chr_sizes"



def count_bam(bamfile, bed_file, output, genome_sizes, use_fast_count=True, verbose=True):
    reads = pysam.AlignmentFile(bamfile)
    read_chrs = set(reads.references)
    bed_regions = pd.read_table(bed_file, header=None)
    bed_regions = bed_regions[bed_regions.columns[:3]]
    bed_regions.columns = "chr start end".split()
    counts = [(reads.count(row.chr, row.start, row.end) if (row.chr in read_chrs) else 0) for _, row in bed_regions.iterrows()]
    bed_regions['count'] = counts
    bed_regions.to_csv(output, header=None, index=None, sep="\t")

count_bam(bamfile, bed_file, output, genome_sizes)

The error I get is:

ValueError: Length mismatch: Expected axis has 1 elements, new values have 3 elements

This is after I made the required file in the function global variables. Before, the error I was getting was:

TypeError: count_bam() missing 3 required positional arguments: 'bed_file', 'output', and 'genome_sizes'

I feel this has something to do with argparse. It reads the 1st required argument (bamfile) but doesn't register the other 3.

Any help would be greatly appreciated.