def _post(request):
"""
Post a sequence and run the sequence through blast and orf detection.
Expects: db and sequence
Response: JSON list of features
"""
db_name = request.REQUEST['db'].strip()
sequence = features.clean_dna_sequence(request.REQUEST['sequence'])
# feature detection
feature_list = features.blast(sequence, db_name)
# restriction site search
cutter_list = features.find_restriction_sites(sequence)
# ORFs and tags
orf_list, tag_list = orfs.detect_orfs_and_tags(sequence)
res = [x.to_dict() for x in feature_list+cutter_list+orf_list+tag_list]
# now sort everything by start
res.sort(cmp=lambda x,y:cmp(int(x['start']),int(y['start'])))
res = [len(sequence),res,sequence]
j = json.JSONEncoder().encode(res)
if 'jsonp' in request.REQUEST:
j = request.REQUEST['jsonp']+'('+j+')'
http_res = HttpResponse(j,mimetype="text/javascript",status=httplib.OK)
else:
# technically we should be returning "application/json", but in that
# case browsers force user to download into a file, and for debugging
# we want to be able to see the JSON list in browser. looks like most
# browsers will handle JSON sent back as text/html anyways.
if request.is_ajax():
http_res = HttpResponse(j,mimetype="application/json",status=httplib.OK)
else:
http_res = HttpResponse(j,status=httplib.OK)
# allow cross origin API calls
http_res['Access-Control-Allow-Origin'] = '*'
http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
http_res['Access-Control-Max-Age'] = 1000
return http_res
def _post(params, is_ajax):
"""
Post a sequence and run the sequence through blast and orf detection.
Expects: db and sequence
Response: JSON list of features
"""
from hippo.models import Feature_Database
is_gb = False
db_name = params['db'].strip()
db = Feature_Database.objects.get(name=db_name)
sequence = params['sequence']
gb_features = []
# parse genbank
if sequence.strip().startswith('LOCUS'):
is_gb = True
try:
sequence, gb_features = gb.parse_genbank(sequence.lstrip())
except Exception as e:
sequence = ""
gb_features = []
# clean sequence
input_type = params['input'] if 'input' in params else 'dna'
if input_type in ['protein']:
sequence = clean_sequence(sequence, alphabet=IUPAC.protein)
else:
sequence = clean_sequence(sequence)
feature_list = gb_features
gbonly = 'gbonly' in params and params['gbonly'] in ['1', 'true', 'True']
blastonly = 'blastonly' in params and params['blastonly'] in [
'1', 'true', 'True'
]
if not is_gb or gbonly is False:
args = {}
if 'identity_threshold' in params:
args['identity_threshold'] = float(params['identity_threshold'])
if 'feature_threshold' in params:
args['feature_threshold'] = float(params['feature_threshold'])
circular = True
if 'circular' in params and str(
params['circular']).strip().lower() in ['false', 0, '0']:
circular = False
# feature detection
feature_list += features.blast(sequence,
db,
input_type=input_type,
protein=False,
circular=circular,
**args)
feature_list += features.blast(sequence,
db,
input_type=input_type,
protein=True,
circular=circular,
**args)
if input_type == 'dna' and blastonly is False:
# restriction site search
feature_list += features.find_restriction_sites(sequence,
circular=circular)
# ORFs and tags
orf_list, tag_list = orfs.detect_orfs_and_tags(sequence,
circular=circular)
feature_list += orf_list
feature_list += tag_list
res = [x.to_dict() for x in feature_list]
# print 'returning %s' % (res,)
# now sort everything by start
res.sort(
cmp=lambda x, y: cmp(int(x['query_start']), int(y['query_start'])))
res = [len(sequence), res, sequence]
j = json.JSONEncoder().encode(res)
if 'jsonp' in params:
j = params['jsonp'] + '(' + j + ')'
http_res = HttpResponse(j,
mimetype="text/javascript",
status=httplib.OK)
else:
# technically we should be returning "application/json", but in that
# case browsers force user to download into a file, and for debugging
# we want to be able to see the JSON list in browser. looks like most
# browsers will handle JSON sent back as text/html anyways.
if is_ajax:
http_res = HttpResponse(j,
mimetype="application/json",
status=httplib.OK)
else:
http_res = HttpResponse(j, status=httplib.OK)
# allow cross origin API calls
http_res['Access-Control-Allow-Origin'] = '*'
http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
http_res['Access-Control-Max-Age'] = 1000
return http_res
def _post(params, is_ajax):
"""
Post a sequence and run the sequence through blast and orf detection.
Expects: db and sequence
Response: JSON list of features
"""
from hippo.models import Feature_Database
is_gb = False
db_name = params['db'].strip()
db = Feature_Database.objects.get(name=db_name)
sequence = params['sequence']
gb_features = []
# parse genbank
if sequence.strip().startswith('LOCUS'):
is_gb = True
try:
sequence, gb_features = gb.parse_genbank(sequence.lstrip())
except Exception as e:
sequence = ""
gb_features = []
# clean sequence
input_type = params['input'] if 'input' in params else 'dna'
if input_type in ['protein']:
sequence = clean_sequence(sequence, alphabet=IUPAC.protein)
else:
sequence = clean_sequence(sequence)
feature_list = gb_features
gbonly = 'gbonly' in params and params['gbonly'] in ['1', 'true', 'True']
blastonly = 'blastonly' in params and params['blastonly'] in ['1', 'true', 'True']
if not is_gb or gbonly is False:
args = {}
if 'identity_threshold' in params:
args['identity_threshold'] = float(params['identity_threshold'])
if 'feature_threshold' in params:
args['feature_threshold'] = float(params['feature_threshold'])
circular = True
if 'circular' in params and str(params['circular']).strip().lower() in ['false', 0, '0']:
circular = False
# feature detection
feature_list += features.blast(sequence, db, input_type=input_type, protein=False, circular=circular, **args)
feature_list += features.blast(sequence, db, input_type=input_type, protein=True, circular=circular, **args)
if input_type == 'dna' and blastonly is False:
# restriction site search
feature_list += features.find_restriction_sites(sequence, circular=circular)
# ORFs and tags
orf_list, tag_list = orfs.detect_orfs_and_tags(sequence, circular=circular)
feature_list += orf_list
feature_list += tag_list
res = [x.to_dict() for x in feature_list]
# print 'returning %s' % (res,)
# now sort everything by start
res.sort(cmp=lambda x,y:cmp(int(x['query_start']),int(y['query_start'])))
res = [len(sequence),res,sequence]
j = json.JSONEncoder().encode(res)
if 'jsonp' in params:
j = params['jsonp']+'('+j+')'
http_res = HttpResponse(j,mimetype="text/javascript",status=httplib.OK)
else:
# technically we should be returning "application/json", but in that
# case browsers force user to download into a file, and for debugging
# we want to be able to see the JSON list in browser. looks like most
# browsers will handle JSON sent back as text/html anyways.
if is_ajax:
http_res = HttpResponse(j,mimetype="application/json",status=httplib.OK)
else:
http_res = HttpResponse(j,status=httplib.OK)
# allow cross origin API calls
http_res['Access-Control-Allow-Origin'] = '*'
http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
http_res['Access-Control-Max-Age'] = 1000
return http_res