Download, extract and read a gzip file in Python

Just gzip.GzipFile(fileobj=handle) and you'll be on your way -- in other words, it's not really true that "the Gzip library only accepts filenames as arguments and not handles", you just have to use the fileobj= named argument.

I've found this question while searching for methods to download and unzip a gzip file from an URL but I didn't manage to make the accepted answer work in Python 2.7.

Here's what worked for me (adapted from here):

import urllib2
import gzip
import StringIO

def download(url):
    # Download SEED database
    out_file_path = url.split("/")[-1][:-3]
    print('Downloading SEED Database from: {}'.format(url))
    response = urllib2.urlopen(url)
    compressed_file = StringIO.StringIO(response.read())
    decompressed_file = gzip.GzipFile(fileobj=compressed_file)

    # Extract SEED database
    with open(out_file_path, 'w') as outfile:
        outfile.write(decompressed_file.read())

    # Filter SEED database
    # ...
    return

if __name__ == "__main__":    
    download("ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/fasta_files/RF00001.fa.gz")

I changed the target URL since the original one was dead: I just looked for a gzip file served from an ftp server like in the original question.