def query_not_base_sequences():
length = 16569
cursor = SequenceDocument.objects(length__ne=length)
records = []
for r in cursor:
records.append(r)
del cursor
return records
def query_normal_length():
length = 377
cursor = SequenceDocument.objects(length=length)
records = []
for r in cursor:
records.append(r)
del cursor
return records
def save_stats_db(sequence):
rcrs_base_sequence = query_base_sequence('NC_012920')
rsrs_base_sequence = query_base_sequence('RSRS')
doc = SequenceDocument.objects(version=sequence.version)
rcrs_distance = count_distance(sequence.sequence, rcrs_base_sequence.sequence[16023:16400])
doc.update(distance_to_rCRS=rcrs_distance)
rsrs_distance = count_distance(sequence.sequence, rsrs_base_sequence.sequence[16023:16400])
doc.update(distance_to_RSRS=rsrs_distance)
def query_base_sequence(name):
return SequenceDocument.objects(name=name)[0]
def reset_sequence_documents_regions():
for seq_document in SequenceDocument.objects(length=377):
seq_document.delete()
def get_sequences_by_region(region):
return SequenceDocument.objects(region__contains=region).only('sequence')