def test_parse_genome_data_17(self):
"""Verify retrieved flat file data is parsed correctly with no
filepath provided."""
gnm = flat_files.parse_genome_data(self.record, gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "")
with self.subTest():
self.assertEqual(gnm.name, "KatherineG")
def test_parse_genome_data_19(self):
"""Verify retrieved flat file data is parsed correctly with
modified translation table."""
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file",
translation_table=1)
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.translation_table, 1)
def test_parse_genome_data_9(self):
"""Verify retrieved flat file data is parsed correctly with no
references."""
self.annotation_dict.pop("references")
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.authors, "")
def test_parse_genome_data_6(self):
"""Verify retrieved flat file data is parsed correctly with more
than one accession."""
self.annotation_dict["accessions"] = [" ABC123.1 ", "TUV456"]
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.accession, "ABC123")
def test_parse_genome_data_18(self):
"""Verify retrieved flat file data is parsed correctly with no
date provided."""
self.annotation_dict.pop("date")
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
self.exp_date = constants.EMPTY_DATE
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.date, self.exp_date)
def test_parse_genome_data_10(self):
"""Verify retrieved flat file data is parsed correctly with
references that contain no authors."""
ref1 = test_data_utils.create_reference()
ref2 = test_data_utils.create_reference()
self.annotation_dict["references"] = [ref1, ref2]
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.authors, "")
def test_parse_genome_data_8(self):
"""Verify retrieved flat file data is parsed correctly with no
record source."""
self.annotation_dict.pop("source")
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.source, "")
with self.subTest():
self.assertEqual(gnm._source_name, "")
with self.subTest():
self.assertEqual(gnm._source_host_genus, "")
def test_parse_genome_data_20(self):
"""Verify retrieved flat file data is parsed correctly with
id field and host genus field specified as non-standard fields."""
gnm = flat_files.parse_genome_data(
self.record,
self.filepath,
gnm_type="flat_file",
genome_id_field="_description_name",
host_genus_field="_description_host_genus")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.id, "L5")
with self.subTest():
self.assertEqual(gnm.host_genus, "Mycobacterium")
def test_parse_genome_data_11(self):
"""Verify retrieved flat file data is parsed correctly with an
empty sequence."""
print(self.record.seq)
self.record.seq = Seq("")
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.seq, "")
with self.subTest():
self.assertEqual(gnm.length, 0)
with self.subTest():
self.assertEqual(gnm.gc, -1)
def test_parse_genome_data_7(self):
"""Verify retrieved flat file data is parsed correctly with no
record description."""
self.record = SeqRecord(seq=Seq("atgc"),
id="OPQ123.1",
name="XYZ123",
annotations=self.annotation_dict,
features=self.feature_list)
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.description, "")
with self.subTest():
self.assertEqual(gnm._description_name, "")
with self.subTest():
self.assertEqual(gnm._description_host_genus, "")
def test_parse_genome_data_4(self):
"""Verify retrieved flat file data is parsed correctly with no
record id."""
self.record = SeqRecord(
seq=Seq("atgc"),
name="XYZ123",
annotations=self.annotation_dict,
description=self.description,
features=self.feature_list,
)
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file",
genome_id_field="")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.id, "")
with self.subTest():
self.assertEqual(gnm.name, "XYZ123")
def test_parse_genome_data_12(self):
"""Verify retrieved flat file data is parsed correctly with no
CDS features."""
self.feature_list = [
self.seqfeature2, self.seqfeature3, self.seqfeature7
]
self.record.features = self.feature_list
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(len(gnm.cds_features), 0)
with self.subTest():
self.assertEqual(len(gnm.source_features), 2)
with self.subTest():
self.assertEqual(len(gnm.trna_features), 1)
with self.subTest():
self.assertEqual(gnm._cds_features_tally, 0)
def test_parse_genome_data_16(self):
"""Verify retrieved flat file data is parsed correctly with no
features."""
self.record.features = []
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(len(gnm.cds_features), 0)
with self.subTest():
self.assertEqual(len(gnm.source_features), 0)
with self.subTest():
self.assertEqual(len(gnm.trna_features), 0)
with self.subTest():
self.assertEqual(gnm._cds_features_tally, 0)
with self.subTest():
self.assertEqual(gnm._source_features_tally, 0)
with self.subTest():
self.assertEqual(gnm._trna_features_tally, 0)
with self.subTest():
self.assertEqual(gnm._tmrna_features_tally, 0)
def test_parse_genome_data_1(self):
"""Verify retrieved flat file data is parsed correctly."""
gnm = flat_files.parse_genome_data(self.record,
self.filepath,
gnm_type="flat_file")
with self.subTest():
self.assertEqual(gnm.filename, "Phage_ZZZ")
with self.subTest():
self.assertEqual(gnm.name, "KatherineG")
with self.subTest():
self.assertEqual(gnm.organism, self.organism)
with self.subTest():
self.assertEqual(gnm._organism_name, "KatherineG")
with self.subTest():
self.assertEqual(gnm._organism_host_genus, "Gordonia")
with self.subTest():
self.assertEqual(gnm.accession, "ABC123")
with self.subTest():
self.assertEqual(gnm.description, self.description)
with self.subTest():
self.assertEqual(gnm._description_name, "L5")
with self.subTest():
self.assertEqual(gnm._description_host_genus, "Mycobacterium")
with self.subTest():
self.assertEqual(gnm.source, self.source)
with self.subTest():
self.assertEqual(gnm._source_name, "phiC31")
with self.subTest():
self.assertEqual(gnm._source_host_genus, "Streptomyces")
with self.subTest():
self.assertEqual(gnm.authors, "Jane;Doe;Smith")
with self.subTest():
self.assertEqual(gnm.seq, "ATGC")
with self.subTest():
self.assertEqual(gnm.length, 4)
with self.subTest():
self.assertEqual(gnm.gc, 50.00)
with self.subTest():
self.assertEqual(gnm.date, self.exp_date)
with self.subTest():
self.assertEqual(len(gnm.cds_features), 4)
with self.subTest():
self.assertEqual(len(gnm.source_features), 2)
with self.subTest():
self.assertEqual(len(gnm.trna_features), 2)
with self.subTest():
self.assertEqual(len(gnm.tmrna_features), 2)
with self.subTest():
self.assertEqual(gnm._cds_features_tally, 4)
with self.subTest():
self.assertEqual(gnm._source_features_tally, 2)
with self.subTest():
self.assertEqual(gnm._trna_features_tally, 2)
with self.subTest():
self.assertEqual(gnm._tmrna_features_tally, 2)
with self.subTest():
self.assertEqual(gnm.translation_table, 11)
with self.subTest():
self.assertEqual(gnm.id, "KatherineG")
with self.subTest():
self.assertEqual(gnm.host_genus, "Gordonia")
with self.subTest():
self.assertEqual(gnm.type, "flat_file")
with self.subTest():
self.assertEqual(gnm.cds_features[0].genome_id, "KatherineG")
with self.subTest():
self.assertEqual(gnm.cds_features[0].id, "KatherineG_CDS_1")
with self.subTest():
self.assertEqual(gnm.cds_features[1].id, "KatherineG_CDS_4")
with self.subTest():
self.assertEqual(gnm.cds_features[2].id, "KatherineG_CDS_3")
with self.subTest():
self.assertEqual(gnm.cds_features[3].id, "KatherineG_CDS_2")
with self.subTest():
self.assertEqual(gnm.cds_features[0].start, 2)
with self.subTest():
self.assertEqual(gnm.cds_features[0].stop, 10)
with self.subTest():
self.assertEqual(gnm.cds_features[0].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.cds_features[1].start, 152829)
with self.subTest():
self.assertEqual(gnm.cds_features[1].stop, 4)
with self.subTest():
self.assertEqual(gnm.cds_features[1].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.cds_features[2].start, 9)
with self.subTest():
self.assertEqual(gnm.cds_features[2].stop, 50)
with self.subTest():
self.assertEqual(gnm.cds_features[3].start, 9)
with self.subTest():
self.assertEqual(gnm.cds_features[3].stop, 30)
with self.subTest():
self.assertEqual(gnm.source_features[0].genome_id, "KatherineG")
with self.subTest():
self.assertEqual(gnm.source_features[0].start, 1)
with self.subTest():
self.assertEqual(gnm.source_features[0].stop, 11000)
with self.subTest():
self.assertEqual(gnm.source_features[0].id, "KatherineG_SRC_2")
with self.subTest():
self.assertEqual(gnm.source_features[1].id, "KatherineG_SRC_1")
with self.subTest():
self.assertEqual(gnm.trna_features[0].start, 5000)
with self.subTest():
self.assertEqual(gnm.trna_features[0].stop, 6000)
with self.subTest():
self.assertEqual(gnm.trna_features[0].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.trna_features[0].id, "KatherineG_TRNA_1")
with self.subTest():
self.assertEqual(gnm.trna_features[1].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.trna_features[1].id, "KatherineG_TRNA_2")
with self.subTest():
self.assertEqual(gnm.tmrna_features[0].start, 50000)
with self.subTest():
self.assertEqual(gnm.tmrna_features[0].stop, 60000)
with self.subTest():
self.assertEqual(gnm.tmrna_features[0].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.tmrna_features[0].id, "KatherineG_TMRNA_1")
with self.subTest():
self.assertEqual(gnm.tmrna_features[1].genome_length, 4)
with self.subTest():
self.assertEqual(gnm.tmrna_features[1].id, "KatherineG_TMRNA_2")
