def test_ignore_equal(self):
p = AttributesParser('=', ignore=['chromosome', 'junk'])
record = 'chromosome=1;ID=id0;junk=drawer'
t = list(p.tokenize(record))
self.assertEqual(t, [
'chromosome', '=', '1', ';', 'ID', '=', 'id0', ';', 'junk', '=',
'drawer'
])
attributes = p(record)
self.assertEqual(attributes, 1)
self.assertIn('ID', p.terms)
self.assertEqual(p.terms['ID'][0], 'id0')
self.assertNotIn('chromosome', p.terms)
self.assertEqual(p.reserved['chromosome'], 0)
def test_numeric_gtf(self):
p = AttributesParser()
attributes = p('exon_number 1')
self.assertEqual(attributes, 1)
self.assertIn('exon_number', p.terms)
self.assertEqual(p.terms['exon_number'], {0: 1})
self.assertIsInstance(p.terms['exon_number'][0], int)
def test_simple_gtf(self):
p = AttributesParser()
attributes = p('gene_id "gene1"')
self.assertEqual(attributes, 1)
self.assertIn('gene_id', p.terms)
self.assertEqual(p.terms['gene_id'], {0: 'gene1'})
self.assertIsInstance(p.terms['gene_id'][0], str)
def test_multi_value_gff(self):
p = AttributesParser('=')
attributes = p('gene_id=gene1;transcript_id=transcript1;exon_number=1')
self.assertEqual(attributes, 3)
line_no = 0
for name, expected, attribute_type in [('gene_id', 'gene1', str),
('transcript_id', 'transcript1',
str), ('exon_number', 1, int)]:
self.assertIn(name, p.terms)
self.assertEqual(p.terms[name], {line_no: expected})
self.assertIsInstance(p.terms[name][line_no], attribute_type)
def test_grcm38(self):
p = AttributesParser('=')
attributes = p(
'ID=id0;Dbxref=taxon:10090;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=C57BL/6J'
)
self.assertEqual(attributes, 8)
line_no = 0
for name, expected, attribute_type in [
('ID', 'id0', str),
('Dbxref', 'taxon:10090', str),
('Name', 1, int),
('chromosome1', 1, int),
('gbkey', 'Src', str),
('genome', 'chromosome', str),
('mol_type', 'genomic DNA', str),
]:
self.assertIn(name, p.terms)
self.assertEqual(p.terms[name], {line_no: expected})
self.assertIsInstance(p.terms[name][line_no], attribute_type)
def test_gff_extra_semicolons(self):
p = AttributesParser('=')
t = list(p.tokenize(' a=1;; b="b"; '))
self.assertEqual(t, ['a', '=', '1', ';', 'b', '=', '"b"', ';'])
def test_gtf_extra_spaces(self):
p = AttributesParser(' ')
t = list(p.tokenize(' a 1; b "b"; '))
self.assertEqual(t, ['a', ' ', '1', ';', 'b', ' ', '"b"', ';'])
def test_empty(self):
p = AttributesParser()
attributes = p('')
self.assertEqual(attributes, 0)
def test_embedded_sep(self):
p = AttributesParser(' ')
t = list(p.tokenize('a "b;c"; d 1'))
self.assertEqual(t, ['a', ' ', '"b;c"', ';', 'd', ' ', '1'])
def test_quoting_missing(self):
p = AttributesParser(' ')
self.assertRaises(ValueError, list, p.tokenize('a "b'))
def test_gff_value_with_spaces(self):
p = AttributesParser('=')
t = list(p.tokenize('mol_type=genomic DNA'))
self.assertEqual(t, ['mol_type', '=', 'genomic DNA'])