def get_dict_from_unfiltered_with_sequences(self) -> dict:
try:
dict_with_genes = {}
mongo_dao_retriever = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT), Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_UNFILTERED)
dict_with_genes = mongo_dao_retriever.get_all_gene_objects_as_dict(
)
deep_copy_dict_with_genes = deepcopy(dict_with_genes)
for id_gene, sequence in deep_copy_dict_with_genes.items():
if sequence is None:
del dict_with_genes[id_gene]
return dict_with_genes
except Exception as error:
print('Caught exception getting unfiltered sequences (to dict):' +
repr(error))
def get_list_of_ids_from_mongo_without_sequence(self) -> list:
list_of_just_ids = None
try:
list_of_just_ids = []
mongo_dao_retriever = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT), Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_UNFILTERED)
list_of_gene_objets = mongo_dao_retriever.get_all_gene_objects_as_list(
)
for gene_object in list_of_gene_objets:
if gene_object.sequence is None:
gene_id = gene_object.gene_id
list_of_just_ids.append(gene_id)
return list_of_just_ids
except Exception as error:
print(
'Caught exception when getting all ids from mongo as list without sequence (unfiltered): '
+ repr(error))
def delete_filtered_collection(self) -> None:
try:
mongo_dao_retriever_filtered = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT), Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_FILTERED)
mongo_dao_retriever_filtered.delete_collection()
except Exception as error:
print('Caught exception when removing filtered collection' +
repr(error))
def insert_filtered_dict_in_filtered_collection(
self, filtered_dict: dict) -> None:
try:
mongo_dao_manager = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT), Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_FILTERED)
mongo_dao_manager.insert_gene_document_from_non_object_dict(
filtered_dict)
except Exception as error:
print(
'Caught exception while inserting filtered sequences in mongo collection'
+ repr(error))
def update_genes_from_dict(self, dict_of_genes: dict) -> None:
try:
if dict_of_genes is not None:
mongo_dao_retriever = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT),
Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_UNFILTERED)
for id_ncbi, sequence in dict_of_genes.items():
ncbi_object_to_update = GeneDTO()
ncbi_object_to_update.gene_id = id_ncbi
ncbi_object_to_update.sequence = sequence
mongo_dao_retriever.update_gene_element_from_object(
ncbi_object_to_update, False)
except Exception as error:
print(
'Caught exception when getting all ids from mongo as list: ' +
repr(error))
def export_filtered_genes_collection_to_fasta(self,
fasta_name: str) -> None:
try:
mongo_dao_retriever = GeneDAO(
MongoClient(Constants.MONGODB_HOST,
Constants.MONGODB_PORT), Constants.MONGODB_DB_NAME,
Constants.MONGODB_COLLECTION_FILTERED)
list_of_seqrecords = mongo_dao_retriever.get_list_of_seqrecords_from_collection(
)
if list_of_seqrecords is None:
print(Constants.MSG_WARNING_FILTERED_COLLECTION_EMPTY)
raise Exception
SeqIO.write(list_of_seqrecords, fasta_name + ".fasta", "fasta")
except Exception as error:
print(
'Caught exception when exporting all data to fasta from filtered collection: '
+ repr(error))