Using argparse to for filename input

Question

Hi I'm trying to use argparse for filename input from command line but I'm struggling to get it working.

I want to take a string passed from the command line (-d) which corresponds to a filename (datbase.csv) and store it in the variable inputargs.snp_database_location.

This gets taken as input to my load_search_snaps function as shown in my code below which opens the file and does stuff (pseudocode) to it.

    import csv, sys, argparse

    parser = argparse.ArgumentParser(description='Search a list of variants against the in house database')
    parser.add_argument('-d', '--database',
        action='store',
        dest='snp_database_location',
        type=str,
        nargs=1,
        help='File location for the in house variant database',
        default='Error: Database location must be specified')

    inputargs = parser.parse_args()

    def load_search_snps(input_file):
        with open(input_file, 'r+') as varin:
            id_store_dictgroup = csv.DictReader(varin)
            #do things with id_store_dictgroup                                                                          
        return result

    load_search_snps(inputargs.snp_database_location)

using the command in bash:

python3 snp_freq_V1-0_export.py -d snpstocheck.csv

I get the following error when I try and pass it a regular csv file from the same directory using command line:

File "snp_freq_V1-0_export.py", line 33, in load_search_snps with open(input_file, 'r+') as varin: TypeError: invalid file: ['snpstocheck.csv']

If I feed the filepath in from within the script it works perfectly. As far as I can tell I get a string for snp_database_location which matches the filename string, but then I get the error. What am I missing that's giving the type error?

Answer 1

nargs=1 makes inputargs.snp_database_location a list (with one element), not a string.

In [49]: import argparse

In [50]: parser = argparse.ArgumentParser()

In [51]: parser.add_argument('-d', nargs=1)
Out[51]: _StoreAction(option_strings=['-d'], dest='d', nargs=1, const=None, default=None, type=None, choices=None, help=None, metavar=None)

In [52]: args = parser.parse_args(['-d', 'snpstocheck.csv'])

In [53]: args.d
Out[53]: ['snpstocheck.csv']

To fix, remove nargs=1.