def test_read_file(self):
to = {
'FBgn0026615':
GeneAnnotation(
'FBgn0026615', [
TermAssociation(
'GO:0005737', {
GAF20FIELDS[3]: [],
GAF20FIELDS[5]: ['FB:FBrf0106275'],
GAF20FIELDS[6]: 'IDA',
GAF20FIELDS[7]: [],
GAF20FIELDS[8]: 'C',
GAF20FIELDS[13]: '20060803',
GAF20FIELDS[14]: 'FlyBase'
}),
TermAssociation(
'GO:0045177', {
GAF20FIELDS[3]: [],
GAF20FIELDS[5]: ['FB:FBrf0106275'],
GAF20FIELDS[6]: 'IDA',
GAF20FIELDS[7]: [],
GAF20FIELDS[8]: 'C',
GAF20FIELDS[13]: '20060803',
GAF20FIELDS[14]: 'FlyBase'
})
], {
GAF20FIELDS[0]: 'FB',
GAF20FIELDS[2]: '10-4',
GAF20FIELDS[9]: '10-4',
GAF20FIELDS[10]: [],
GAF20FIELDS[11]: 'gene_product',
GAF20FIELDS[12]: ['taxon:7227'],
GAF20FIELDS[15]: [],
GAF20FIELDS[16]: ''
}),
'FBgn0043467':
GeneAnnotation(
'FBgn0043467', [
TermAssociation(
'GO:0048149', {
GAF20FIELDS[3]: [],
GAF20FIELDS[5]:
['FB:FBrf0131396', 'PMID:11086999'],
GAF20FIELDS[6]: 'IMP',
GAF20FIELDS[7]: [],
GAF20FIELDS[8]: 'P',
GAF20FIELDS[13]: '20060803',
GAF20FIELDS[14]: 'FlyBase'
})
], {
GAF20FIELDS[0]: 'FB',
GAF20FIELDS[2]: '064Ya',
GAF20FIELDS[9]: '064Ya',
GAF20FIELDS[10]: [],
GAF20FIELDS[11]: 'gene_product',
GAF20FIELDS[12]: ['taxon:7227'],
GAF20FIELDS[15]: [],
GAF20FIELDS[16]: ''
})
}
with open('Ontology/GoaIO/correct20.fb', 'r') as f:
objs = GafReader(f).read()
self.assertEqual(to, objs)
def test_incorrect_line_len(self):
with open('Ontology/GoaIO/bad_line.fb', 'r') as f:
it = GafReader(f)
with self.assertRaises(ValueError):
it.read()
def test_incorrect_line_len(self):
with open("Ontology/GoaIO/bad_line.fb", "r") as f:
it = GafReader(f)
with self.assertRaises(ValueError):
it.read()
def test_no_version(self):
with open('Ontology/GoaIO/no_ver.fb', 'r') as f:
it = GafReader(f, assoc_format="in_mem_sql")
with self.assertRaises(ValueError):
it.read()
def test_no_version(self):
with open("Ontology/GoaIO/no_ver.fb", "r") as f:
it = GafReader(f, assoc_format="in_mem_sql")
with self.assertRaises(ValueError):
it.read()