import urllib.parse as urllib
import urllib.request as urllib2
from urllib.request import urlopen, Request
from urllib.error import URLError
import json
import os.path as op
def manual_get_pfam_annotations(seq, outpath, searchtype='phmmer', force_rerun=False):
"""Retrieve and download PFAM results from the HMMER search tool.
Args:
seq:
outpath:
searchtype:
force_rerun:
Returns:
Todo:
* Document and test!
"""
if op.exists(outpath):
with open(outpath, 'r') as f:
json_results = json.loads(json.load(f))
else:
fseq = '>Seq\n' + seq
if searchtype == 'phmmer':
parameters = {'seqdb': 'pdb', 'seq': fseq}
if searchtype == 'hmmscan':
parameters = {'hmmdb': 'pfam', 'seq': fseq}
enc_params = urllib.urlencode(parameters).encode('utf-8')
request = urllib2.Request('http://www.ebi.ac.uk/Tools/hmmer/search/{}'.format(searchtype), enc_params)
url = (urllib2.urlopen(request).geturl() + '?output=json')
request = str(url)
request_read = urlopen(request).read().decode("utf-8")
with open(outpath, 'w') as f:
json.dump(request_read, f)
json_results = json.loads(request_read)
return json_results['results']['hits']
