def test_seq_subset_load_from_all_genes(self):
seqfile_ops.write_genbank(self.gbk_filename, self.record)
subset_mode = 'features'
subset_args = {'types': ('genes'), 'tags': {}}
subset, subset_file = dataset_load.seq_subset_load(self.gbk_filename,
subset_mode,
subset_args)
self.assertIs(len(subset), 2)
def test_seq_subset_load_from_cds_by_locus_tag(self):
seqfile_ops.write_genbank(self.gbk_filename, self.record)
subset_mode = 'features'
subset_args = {'types': ('CDS'), 'tags': {'locus_tag': ['locustag 1',
'locustag 4']}}
subset, subset_file = dataset_load.seq_subset_load(self.gbk_filename,
subset_mode,
subset_args)
self.assertIs(len(subset), 1)
self.assertEqual(subset[0].id, 'temp_5-10')
def test_seq_subset_load_from_mixed_features(self):
seqfile_ops.write_genbank(self.gbk_filename, self.record)
subset_mode = 'features'
subset_args = {'types': ('CDS', 'gene'), 'tags': {'locus_tag':
('locustag 3'),
'product':
(('product 2'))}}
subset, subset_file = dataset_load.seq_subset_load(self.gbk_filename,
subset_mode,
subset_args)
self.assertIs(len(subset), 2)
def test_surefmt_load_gbk2fas(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
fas_record = seqfile_ops.surefmt_load(self.gbk_filename,
'fasta', generic_dna)
self.assertEqual(fas_record.id, self.record.id)
def setUp(self):
# create temp directory
self.temp_dir = "tests/temp_data/"
os.mkdir(self.temp_dir)
# create a sequence record with genbank features
self.seq = Seq("AATTTAATGGCGCAGGCTAGGAGAGAGATTTTTGGCGCTCGCGGGGCGGGG", generic_dna)
self.feat_cds1 = SeqFeature(
FeatureLocation(5, 10), strand=1, type="CDS", qualifiers={"locus_tag": "locustag 1", "product": "product 1"}
)
self.feat_cds2 = SeqFeature(
FeatureLocation(22, 40),
strand=-1,
type="CDS",
qualifiers={"locus_tag": "locustag 2", "product": "product 2"},
)
self.feat_gene1 = SeqFeature(
FeatureLocation(5, 10),
strand=-1,
type="gene",
qualifiers={"locus_tag": "locustag 3", "product": "product 3"},
)
self.feat_gene2 = SeqFeature(
FeatureLocation(22, 40),
strand=-1,
type="gene",
qualifiers={"locus_tag": "locustag 4", "product": "product 4"},
)
self.features = [self.feat_cds1, self.feat_cds2, self.feat_gene1, self.feat_gene2]
self.record = SeqRecord(
self.seq, id="temp", name="temp_name", description="temporary genbank record", features=self.features
)
self.filename = self.temp_dir + "temp_in.gbk"
self.count = seqfile_ops.write_genbank(self.filename, self.record)
def test_write_and_load_single_genbank(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
gbk_record = seqfile_ops.load_genbank(self.gbk_filename)
self.assertEqual(gbk_record.id, self.record.id)
# check features
for index in range (0,1):
self.assertEqual(gbk_record.features[index].type,
self.record.features[index].type)
def test_load_agnostic_gbk(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
gbk_record, type = seqfile_ops.load_agnostic(self.gbk_filename)
self.assertEqual(gbk_record.id, self.record.id)
self.assertEqual(type, 'genbank')
# check features
for index in range (0,1):
self.assertEqual(gbk_record.features[index].type,
self.record.features[index].type)
def test_surefmt_load_gbk2gbk(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
gbk_record = seqfile_ops.surefmt_load(self.gbk_filename,
'genbank', generic_dna)
self.assertEqual(gbk_record.id, self.record.id)
# check features
for index in range (0,1):
self.assertEqual(gbk_record.features[index].type,
self.record.features[index].type)
def test_seqfile_format_gbk(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
format, name = seqfile_ops.seqfile_format(self.gbk_filename)
self.assertEqual(format, 'genbank')
