Here's a slightly changed version of this script.

I changed line 42 from 'title':'NCBI Entrez Gene' to 'title':'NCBI Gene' ).

And line 76 from res_dict = fill_dict(gene_list=args.input) to res_dict = fill_dict(gene_list=args.list)

Here's an example of how it works:

python3 get_from_gene_cards.py --list ensembl_ids.txt

Where ensembl_ids.txt looks like this:

ENSG00000018607
ENSG00000042304
ENSG00000064489

.

#!/usr/bin/python3

from bs4 import BeautifulSoup
import requests
import html
import time
import argparse

'''
Made in a boring day by @danilotat. Enjoy
'''
def get_symbol(html_file, ensgid):
    soup = BeautifulSoup(html_file, 'html.parser')
    try:
        title_tag = soup.find('title')
        if title_tag and title_tag.contents:
            symbol_tag = title_tag.contents[0]
            symbol = symbol_tag.split(' ')[0]
            if symbol == ensgid:
                return 'NaN'
            else:
                return symbol
        else:
            return 'NaN'
    except AttributeError:
        print('Genecards is blocking your requests. Please try again later with less geneid')
        exit()

def gene_card_request(ensgid):
    ''' 
    Passing Ensembl gene id, return its webpage on Genecards
    '''
    url_to_request = 'https://www.genecards.org/cgi-bin/carddisp.pl?gene=' + ensgid
    headers = {'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/39.0.2171.95 Safari/537.36'}
    r = requests.get(url_to_request, headers=headers)
    gene_card_html = html.unescape(r.text)
    return gene_card_html

def get_entrez(html_file):
    ''' 
    Given a valid Ensembl gene id, returns Entrez gene id
    '''
    soup = BeautifulSoup(html_file, 'html.parser')
    entrez_href = soup.find_all('a', {'title': 'NCBI Gene'})
    # usually it will return redundant refer: we'll take just the first of them
    try:
        link = entrez_href[0]
        ncbi_url = link.get('href')
        entrez_id = ncbi_url.split('/')[-1]
        return entrez_id
    except IndexError:
        # empty list: no Entrez ID 
        return "NaN"

def fill_dict(gene_list):
    ''' Fill a dict with Ensembl geneid, entrez, symbol
    '''
    conv_dict = {}
    with open(gene_list, 'r') as engid_list:
        for line in engid_list:
            ensgid = line.rstrip()
            gcard_page = gene_card_request(ensgid)
            entrez_id = get_entrez(gcard_page)
            symbol = get_symbol(gcard_page, ensgid)
            conv_dict.setdefault(ensgid, []).extend([entrez_id, symbol])
            time.sleep(5)
    return conv_dict

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="Giving a list of valid Ensembl gene ID, query GeneCards to get Entrez and symbols.")
    parser.add_argument("--list", help="Input list of Ensembl gene ID, one per line.")
    parser.add_argument("--gene", help="Single gene mode")
    args = parser.parse_args()

    if args.list is None and args.gene is None:
        parser.print_help()
        exit()

    if args.gene is None:
        res_dict = fill_dict(gene_list=args.list)
        for ensgid in res_dict.keys():
            print('{},{},{}'.format(ensgid, res_dict[ensgid][0], res_dict[ensgid][1]))
    else:
        gcard_page = gene_card_request(args.gene)
        print('{},{},{}'.format(args.gene, get_entrez(gcard_page), get_symbol(gcard_page, args.gene)))