# print reps
qIndex = 0
qSeqs = [74, 1, 2, 3, 4, 5, 6, 7, 8, 9]
qStarts = [0, 2, 3, 20, 1, 1, 3, 3, 1, 1]
qEnds = [95, 60, 50, 70, 80, 59, 99, 40, 77, 100]
#num_test = len(qSeqs)
num_test = 4
for i in range(num_test):
qSeq = qSeqs[i]
qStart = qStarts[i]
qEnd = qEnds[i]
dist, seq, start, end = onex.findSimilar(dbIndex, qIndex, qSeq, qStart,
qEnd, 0, warp)
print """Find subsequence in database {} that is similar to subsequence:
qIndex = {}
qSeq = {}
qStart = {}
qEnd = {}""".format(dbIndex, qIndex, qSeq, qStart, qEnd)
print "Distance = {} Sequence = {} Start = {} End = {}".format(
dist, seq, start, end)
querySequence = onex.getSubsequence(qIndex, qSeq, qStart, qEnd)
matchSequence = onex.getSubsequence(dbIndex, seq, start, end)
print "Query:\n{}".format(querySequence)
print "Match:\n{}".format(matchSequence)
def api_find_best_match():
request_id = request.args.get('requestID', type=int)
ds_collection_index = request.args.get('dsCollectionIndex', type=int)
q_find_with_custom_query = request.args.get('qFindWithCustomQuery',
0,
type=int)
q_seq = request.args.get('qSeq', type=int)
q_start = request.args.get('qStart', type=int)
q_end = request.args.get('qEnd', type=int)
if q_start > q_end or q_start < 0 or q_end < 0:
raise InvalidUsage('Invalid starting and ending position')
with lock:
if not (ds_collection_index == current_collection_index):
raise InvalidUsage(
'Dataset {} is not loaded yet'.format(ds_collection_index))
# Index of the dataset containing the query, by default set to the same dataset
# where the best match will be searched from
q_ds_index = current_ds_index
if q_find_with_custom_query:
if current_q_index == -1:
raise InvalidUsage('No custom query is loaded')
# If find with custom query, set to the dataset containing the custom query
q_ds_index = current_q_index
# Get number of sequences in the database containing the query
q_ds_length = onex.getDatasetSeqCount(q_ds_index)
if q_seq < 0 or q_seq >= q_ds_length:
raise InvalidUsage('Sequence index is out of bound')
seq_length = onex.getDatasetSeqLength(q_ds_index)
if q_start >= seq_length or q_end >= seq_length:
raise InvalidUsage('Invalid starting and ending position')
if q_find_with_custom_query:
app.logger.debug(
'Look for best match with sequence %d (%d:%d) in the custom query',
q_seq, q_start, q_end)
else:
app.logger.debug(
'Look for best match with sequence %d (%d:%d) in dataset %d',
q_seq, q_start, q_end, current_collection_index)
r_dist, r_seq, r_start, r_end = \
onex.findSimilar(current_ds_index, q_ds_index, q_seq, q_start, q_end, 0, -1)
group_index = onex.getGroupIndex(current_ds_index, r_seq, r_start,
r_end)
app.logger.debug('Result group index: (%d, %d)', group_index[0],
group_index[1])
result = _to_string(
onex.getSubsequence(current_ds_index, r_seq, r_start, r_end))
warpingPath = onex.getWarpingPath(q_ds_index, q_seq, q_start, q_end,
current_ds_index, r_seq, r_start,
r_end)
return jsonify(result=result,
groupIndex=group_index,
warpingPath=warpingPath,
dist=r_dist,
dsName=datasets[current_collection_index],
seq=r_seq,
start=r_start,
end=r_end,
requestID=request_id)