# Open the wanted_accessions file and read in each accession, stripping newline
# characters, and adding each accesion into the list accession_ids
accession_IDs = []
with open(wanted_accessions, "r") as accessions:
accessions_list = accessions.readlines()
for line in accessions_list:
line = line.rstrip()
accession_IDs.append(line)
# Join each accession id into a string seperated by '+' characters for URL
# construction below
gene_IDs = "+".join(accession_IDs)
# Construct the URL with wanted accessions, Example URL:
# http://iptol-api.iplantcollaborative.org/onekp/v1/orthogroups?
# accession=AT4G04640+AT1G15700+AT4G09650+AT2G07707+AT4G32260
# &token=1463695387322_wsMwZ5o5EmmC1Oan
# &format=zip
wanted_url = base_url + "orthogroups?" + "accession=" + gene_IDs + "&token=" + auth_token + "&format=" + file_format
# Retrieve the wanted orthogroups and if an ok status code is given by the
# server, extract the zipped archive. If a bad status code is given by the
# server, print the attempted URL and the bad status code.
orthogroup_file = requests.get(wanted_url, auth=HTTPDigestAuth("1kp-data", "1kp-rna1"))
if orthogroup_file.status_code == requests.codes.ok:
# print 'Success using this URL:', orthogroup_file.url
orthogroup_file = ZipFile(StringIO(orthogroup_file.content))
orthogroup_file.extractall()
else:
orthogroup_file.raise_for_status()
print "Error using this URL:", orthogroup_file.url
