def test_retrieve_data_3(self):
"""Verify that dictionaries of data are retrieved for a list of two
valid PhageIDs."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, column="PhageID",
id_list=["L5","Trixie"], query=PHAGE_QUERY)
self.assertEqual(len(result_list), 2)
def test_retrieve_data_7(self):
"""Verify that an empty list of CDS data is retrieved
for an invalid PhageID."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, column="PhageID",
id_list=["L5"], query=GENE_QUERY)
self.assertEqual(len(result_list), 0)
def test_retrieve_data_2(self):
"""Verify that an empty list is retrieved for an invalid PhageID."""
result_list = mysqldb_basic.retrieve_data(self.engine1,
column="PhageID",
id_list=["EagleEye"],
query=PHAGE_QUERY)
self.assertEqual(len(result_list), 0)
def test_retrieve_data_4(self):
"""Verify that dictionaries of data are retrieved for a list of three
valid PhageIDs and one invalid PhageID."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, column="PhageID",
id_list=["L5","Trixie","EagleEye","D29"],
query=PHAGE_QUERY)
self.assertEqual(len(result_list), 3)
def test_retrieve_data_1(self):
"""Verify that a dictionary of data is retrieved for a valid PhageID."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, column="PhageID",
id_list=["L5"], query=PHAGE_QUERY)
with self.subTest():
self.assertEqual(len(result_list[0].keys()), 14)
with self.subTest():
self.assertEqual(result_list[0]["PhageID"], "L5")
def test_retrieve_data_6(self):
"""Verify that a list of CDS data is retrieved for a valid PhageID."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, column="PhageID",
id_list=["Trixie"], query=GENE_QUERY)
with self.subTest():
self.assertEqual(len(result_list), 3)
with self.subTest():
self.assertEqual(len(result_list[0].keys()), 13)
with self.subTest():
self.assertEqual(result_list[0]["PhageID"], "Trixie")
def parse_feature_data(engine,
ftr_type,
column=None,
phage_id_list=None,
query=None):
"""Returns Cds objects containing data parsed from a
MySQL database.
:param engine:
This parameter is passed directly to the 'retrieve_data' function.
:type engine: Engine
:param query:
This parameter is passed directly to the 'retrieve_data' function.
:type query: str
:param ftr_type:
Indicates the type of features retrieved.
:type ftr_type: str
:param column:
This parameter is passed directly to the 'retrieve_data' function.
:type column: str
:param phage_id_list:
This parameter is passed directly to the 'retrieve_data' function.
:type phage_id_list: list
:returns: A list of pdm_utils Cds objects.
:rtype: list
"""
result_list = mysqldb_basic.retrieve_data(engine,
column=column,
query=query,
id_list=phage_id_list)
ftrs = []
for data_dict in result_list:
if ftr_type == "cds":
ftr = parse_gene_table_data(data_dict)
elif ftr_type == "trna":
ftr = parse_trna_table_data(data_dict)
elif ftr_type == "tmrna":
ftr = parse_tmrna_table_data(data_dict)
else:
# If the ftr_type is invalid, just take the data dictionary.
# Alternatively it could raise an error.
ftr = data_dict
ftrs.append(ftr)
return ftrs
def test_retrieve_data_8(self):
"""Verify that a list of all CDS data is retrieved when no
PhageID is provided."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, query=GENE_QUERY)
self.assertEqual(len(result_list), 4)
def test_retrieve_data_5(self):
"""Verify that dictionaries of data are retrieved for multiple
valid PhageIDs when no list is provided."""
result_list = mysqldb_basic.retrieve_data(
self.engine1, query=PHAGE_QUERY)
self.assertEqual(len(result_list), 3)
def parse_genome_data(engine, phage_id_list=None, phage_query=None,
gene_query=None, trna_query=None, tmrna_query=None,
gnm_type=""):
"""Returns a list of Genome objects containing data parsed from a MySQL
database.
:param engine:
This parameter is passed directly to the 'retrieve_data' function.
:type engine: Engine
:param phage_query:
This parameter is passed directly to the 'retrieve_data' function
to retrieve data from the phage table.
:type phage_query: str
:param gene_query:
This parameter is passed directly to the 'parse_feature_data' function
to retrieve data from the gene table.
If not None, pdm_utils Cds objects for all of the phage's
CDS features in the gene table will be constructed
and added to the Genome object.
:type gene_query: str
:param trna_query:
This parameter is passed directly to the 'parse_feature_data' function
to retrieve data from the trna table.
If not None, pdm_utils Trna objects for all of the phage's
tRNA features in the trna table will be constructed
and added to the Genome object.
:type trna_query: str
:param tmrna_query:
This parameter is passed directly to the 'parse_feature_data' function
to retrieve data from the tmrna table.
If not None, pdm_utils Tmrna objects for all of the phage's
tmRNA features in the tmrna table will be constructed
and added to the Genome object.
:type tmrna_query: str
:param phage_id_list:
This parameter is passed directly to the 'retrieve_data' function.
If there is at at least one valid PhageID, a pdm_utils genome
object will be constructed only for that phage. If None, or an
empty list, genome objects for all phages in the
database will be constructed.
:type phage_id_list: list
:param gnm_type: Identifier for the type of genome.
:type gnm_type: str
:returns: A list of pdm_utils Genome objects.
:rtype: list
"""
COLUMN = "PhageID"
genome_list = []
result_list1 = mysqldb_basic.retrieve_data(engine, column=COLUMN,
id_list=phage_id_list,
query=phage_query)
for data_dict in result_list1:
gnm = parse_phage_table_data(data_dict, gnm_type=gnm_type)
if gene_query is not None:
cds_list = parse_feature_data(engine, "cds", column=COLUMN,
phage_id_list=[gnm.id],
query=gene_query)
for x in range(len(cds_list)):
cds_list[x].genome_length = gnm.length
gnm.cds_features = cds_list
if trna_query is not None:
trna_list = parse_feature_data(engine, "trna", column=COLUMN,
phage_id_list=[gnm.id],
query=trna_query)
for x in range(len(trna_list)):
trna_list[x].genome_length = gnm.length
gnm.trna_features = trna_list
if tmrna_query is not None:
tmrna_list = parse_feature_data(engine, "tmrna", column=COLUMN,
phage_id_list=[gnm.id],
query=tmrna_query)
for x in range(len(tmrna_list)):
tmrna_list[x].genome_length = gnm.length
gnm.tmrna_features = tmrna_list
genome_list.append(gnm)
return genome_list
