def test_parse_genome_data_10(self):
"""Verify output when seq is False."""
url = "https://phagesdb.org/media/fastas/L5.fasta"
filename = Path(url).stem
data_dict = {
"phage_name": "Trixie",
"pcluster": {
"cluster": "A"
},
"psubcluster": {
"subcluster": "A2"
},
"isolation_host": {
"genus": "Mycobacterium"
},
"genbank_accession": "ABC123",
"fasta_file": url
}
self.gnm = phagesdb.parse_genome_data(data_dict,
gnm_type="phagesdb",
seq=False)
with self.subTest():
self.assertEqual(self.gnm.filename, filename)
with self.subTest():
self.assertEqual(self.gnm.seq, "")
with self.subTest():
self.assertEqual(self.gnm.description, "")
with self.subTest():
self.assertEqual(self.gnm._description_name, "")
with self.subTest():
self.assertEqual(self.gnm._description_host_genus, "")
def test_parse_genome_data_1(self):
"""Verify genome object is parsed from PhagesDB."""
url = "https://phagesdb.org/media/fastas/L5.fasta"
filename = Path(url).stem
data_dict = {
"phage_name": "Trixie",
"pcluster": {
"cluster": "A"
},
"psubcluster": {
"subcluster": "A2"
},
"isolation_host": {
"genus": "Mycobacterium"
},
"genbank_accession": "ABC123",
"fasta_file": url
}
self.gnm = phagesdb.parse_genome_data(data_dict,
gnm_type="phagesdb",
seq=True)
with self.subTest():
self.assertEqual(self.gnm.name, "Trixie")
with self.subTest():
self.assertEqual(self.gnm.id, "Trixie")
with self.subTest():
self.assertEqual(self.gnm.cluster, "A")
with self.subTest():
self.assertEqual(self.gnm.subcluster, "A2")
with self.subTest():
self.assertEqual(self.gnm.host_genus, "Mycobacterium")
with self.subTest():
self.assertEqual(self.gnm.accession, "ABC123")
with self.subTest():
self.assertEqual(self.gnm.filename, filename)
with self.subTest():
self.assertEqual(self.gnm.seq[:8], "GGTCGGTT")
with self.subTest():
self.assertEqual(self.gnm.seq[-8:], "GTCGGTTA")
with self.subTest():
self.assertIsInstance(self.gnm.seq, Seq)
with self.subTest():
self.assertEqual(self.gnm.description, "Mycobacterium phage L5")
with self.subTest():
self.assertEqual(self.gnm._description_name, "L5")
with self.subTest():
self.assertEqual(self.gnm._description_host_genus, "Mycobacterium")
with self.subTest():
self.assertEqual(self.gnm.type, "phagesdb")
with self.subTest():
self.assertIsInstance(self.gnm.misc, dict)
def test_parse_genome_data_6(self):
"""Verify output when there is no genbank_accession key."""
url = "https://phagesdb.org/media/fastas/L5.fasta"
data_dict = {
"phage_name": "Trixie",
"pcluster": {
"cluster": "A"
},
"psubcluster": {
"subcluster": "A2"
},
"isolation_host": {
"genus": "Mycobacterium"
},
"genbank_accession_x": "ABC123",
"fasta_file": url
}
self.gnm = phagesdb.parse_genome_data(data_dict, gnm_type="phagesdb")
self.assertEqual(self.gnm.accession, "")
def test_parse_genome_data_9(self):
"""Verify output when there are multiple errors."""
url = "https://phagesdb.org/media/fastas/L5.fasta"
data_dict = {
"phage_name": "Trixie",
"pcluster_x": {
"cluster": "A"
},
"psubcluster_x": {
"subcluster": "A2"
},
"isolation_host_x": {
"genus": "Mycobacterium"
},
"genbank_accession_x": "ABC123",
"fasta_file_x": url
}
self.gnm = phagesdb.parse_genome_data(data_dict, seq=True)
with self.subTest():
self.assertEqual(self.gnm.name, "Trixie")
with self.subTest():
self.assertEqual(self.gnm.id, "Trixie")
with self.subTest():
self.assertEqual(self.gnm.cluster, "")
with self.subTest():
self.assertEqual(self.gnm.subcluster, "")
with self.subTest():
self.assertEqual(self.gnm.host_genus, "")
with self.subTest():
self.assertEqual(self.gnm.accession, "")
with self.subTest():
self.assertEqual(self.gnm.filename, "")
with self.subTest():
self.assertEqual(self.gnm.seq, "")
with self.subTest():
self.assertEqual(self.gnm.description, "")
with self.subTest():
self.assertEqual(self.gnm._description_name, "")
with self.subTest():
self.assertEqual(self.gnm._description_host_genus, "")
with self.subTest():
self.assertEqual(self.gnm.type, "")