diff --git a/bin/WhatsGNU_get_GenBank_genomes.py b/bin/WhatsGNU_get_GenBank_genomes.py index 42b6cc7..81be19e 100755 --- a/bin/WhatsGNU_get_GenBank_genomes.py +++ b/bin/WhatsGNU_get_GenBank_genomes.py @@ -118,9 +118,6 @@ GCA_LIST.append(line) ######################################## -ctx = ssl.create_default_context() -ctx.check_hostname = False -ctx.verify_mode = ssl.CERT_NONE for GCA in GCA_LIST: try: GCA_ftp_url = GCA_DICT[GCA] #url from assembly_summary_genbank.txt @@ -130,30 +127,18 @@ if ARGS.faa and not ARGS.contigs: faa_file = RESULTS_FOLDER + GCA_acc + '.faa.gz' faa_url = GCA_file_url + '_protein.faa.gz' - faa_file_object = open(faa_file, 'wb') - with closing(request.urlopen(faa_url, context=ctx)) as file_link: - shutil.copyfileobj(file_link, faa_file_object) - faa_file_object.close() + request.urlretrieve(faa_url, faa_file) if ARGS.contigs and not ARGS.faa: contigs_file = RESULTS_FOLDER + GCA_acc + '.fna.gz' contigs_url = GCA_file_url + '_genomic.fna.gz' - contigs_file_object = open(contigs_file, 'wb') - with closing(request.urlopen(contigs_url, context=ctx)) as file_link: - shutil.copyfileobj(file_link, contigs_file_object) - contigs_file_object.close() + request.urlretrieve(contigs_url, contigs_file) if ARGS.faa and ARGS.contigs: - faa_file = PROTEINS_FOLDER + OS_SEPARATOR + GCA_acc + '.faa.gz' + faa_file = RESULTS_FOLDER + GCA_acc + '.faa.gz' faa_url = GCA_file_url + '_protein.faa.gz' - faa_file_object = open(faa_file, 'wb') - with closing(request.urlopen(faa_url, context=ctx)) as file_link: - shutil.copyfileobj(file_link, faa_file_object) - faa_file_object.close() - contigs_file = CONTIGS_FOLDER + OS_SEPARATOR + GCA_acc + '.fna.gz' + request.urlretrieve(faa_url, faa_file) + contigs_file = RESULTS_FOLDER + GCA_acc + '.fna.gz' contigs_url = GCA_file_url + '_genomic.fna.gz' - contigs_file_object = open(contigs_file, 'wb') - with closing(request.urlopen(contigs_url, context=ctx)) as file_link: - shutil.copyfileobj(file_link, contigs_file_object) - contigs_file_object.close() + request.urlretrieve(contigs_url, contigs_file) except: print("Could not get the ftp url for {} from assembly_summary_genbank.txt".format(GCA)) if ARGS.remove: