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test_grammar.py
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test_grammar.py
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from unittest import TestCase
from gnomic import Feature, Organism, Genotype, Ins, Accession, Type, DEFAULT_ORGANISMS, DEFAULT_TYPES, Del, Plasmid, \
Sub, Fusion, Mutation, FeatureTree, FeatureSet
def parse(string):
return Genotype._parse_string(string,
organisms=DEFAULT_ORGANISMS,
types=DEFAULT_TYPES)
class GrammarTestCase(TestCase):
def test_empty_genotype(self):
self.assertEqual([], parse(''))
def test_parse_feature(self):
self.assertEqual(Feature(name='geneA'), Feature.parse('geneA'))
self.assertEqual(Feature(name='A', type=Type('gene')), Feature.parse('gene.A'))
self.assertNotEqual(Feature(name='geneA'), Feature.parse('geneA(x)'))
self.assertEqual(Feature(name='geneA', variant='x'), Feature.parse('geneA(x)'))
self.assertEqual(Feature(name='geneA', variant='wild-type', organism=Organism('foo')),
Feature.parse('foo/geneA+'))
self.assertEqual(Feature(name='geneA', variant='mutant', organism=Organism('foo')), Feature.parse('foo/geneA-'))
def test_parse_simple_insertions(self):
self.assertEqual([
Ins(Feature(name='fooF'))
], parse('+fooF'))
self.assertEqual([
Ins(Feature(name='fooF', accession=Accession(identifier=123, database='FOO')))
], parse('+fooF#FOO:123'))
self.assertEqual([
Ins(Feature(accession=Accession(identifier=123, database='FOO')))
], parse('+#FOO:123'))
self.assertEqual([
Ins(Feature(accession=Accession(identifier='BAR', database='FOO')))
], parse('+#FOO:BAR'))
self.assertEqual([
Ins(Feature(accession=Accession(identifier=123)))
], parse('+#123'))
def test_parse_plasmid_presence(self):
self.assertEqual([Plasmid('pA', None)], parse('(pA)'))
self.assertEqual([Plasmid('pA', None)], parse('pA{}'))
def test_parse_variants(self):
self.assertEqual([
Feature(type=Type('phene'), name='A', variant='wild-type')
], parse('A+'))
self.assertEqual([
Feature(type=Type('phene'), name='A', variant='mutant')
], parse('A-'))
self.assertEqual([
Feature(type=Type('phene'), name='A', variant='custom')
], parse('A(custom)'))
self.assertEqual([
Feature(type=Type('phene'), name='A', variant='first, second')
], parse('A(first, second)'))
self.assertEqual([
Feature(type=Type('phene'),
name='A',
organism=Organism('Escherichia coli'),
variant='wild-type')
], parse('Ec/A+'))
self.assertEqual([
Feature(type=Type('phene'),
name='A',
organism=Organism('Escherichia coli'),
variant='wild-type')
], parse('Ec/A+'))
self.assertEqual([
Feature(type=Type('phene'),
accession=Accession(identifier=123, database='FOO'),
variant='wild-type')
], parse('#FOO:123+'))
def test_parse_simple_deletions(self):
self.assertEqual([
Del(Feature(name='fooF'))
], parse('-fooF'))
self.assertEqual([
Del(Plasmid('pFoo', None))
], parse('-pFoo{}'))
self.assertEqual([
Del(Plasmid('pBar', None))
], parse('-(pBar)'))
changes = parse('-pFoo{fooF}')
self.assertEqual([
Del(Plasmid('pFoo', None))
], changes)
self.assertEqual((
Feature(name='fooF'),
), changes[0].old.contents)
changes = parse('-(pBar barB)')
self.assertEqual([
Del(Plasmid('pBar', None))
], changes)
self.assertEqual((
Feature(name='barB'),
), changes[0].old.contents)
def test_parse_simple_replacements(self):
self.assertEqual([
Sub(Feature(name='fooF'), Feature(name='barB'))
], parse('fooF>barB'))
self.assertEqual([
Sub(Feature(name='fooF'), Feature(name='barB'), multiple=True)
], parse('fooF>>barB'))
self.assertEqual([
Sub(Feature(name='fooF'), Feature(name='barB'),
markers=[Feature(name='marker', variant='wild-type', type=Type('phene'))],
multiple=True)
], parse('fooF>>barB::marker+'))
def test_parse_insert_groups(self):
self.assertEqual([
Ins(FeatureSet(Feature(name='fooF')))
], parse('+{fooF}'))
self.assertEqual([
Ins(FeatureSet(Feature(name='fooF'),
Feature(name='barB'),
Feature(name='bazZ')))
], parse('+{fooF barB bazZ}'))
self.assertEqual([
Ins(FeatureSet(Feature(name='fooF'),
Fusion(Feature(name='barB'), Feature(name='bazZ')),
Feature('lolO')))
], parse('+{fooF barB:bazZ lolO}'))
def test_parse_plasmid_deletions(self):
result = parse('-pFoo{barB, bazZ}')
self.assertEqual([
Del(Plasmid('pFoo', None))
], result)
self.assertEqual((
Feature(name='barB'),
Feature(name='bazZ'),
), result[0].old.contents)
def test_parse_fusion_featureset(self):
self.assertEqual([
Mutation(new=Fusion(Feature(name='featB'), FeatureSet(Feature(name='featC'), Feature(name='featD'))),
old=Feature(name='featA'))
], parse('featA>featB:{featC featD}'))
self.assertEqual([
Mutation(new=Fusion(Feature(name='featB'), FeatureSet(Feature(name='featC')), Feature(name='featD')),
old=Feature(name='featA'))
], parse('featA>featB:{featC}:featD'))
def test_parse_fusion_replacement(self):
self.assertEqual([
Mutation(old=Fusion(Feature(name='featA'), FeatureSet(Feature(name='featB'))),
new=Feature(name='featC'),
multiple=True,
markers=[Feature(variant='wild-type', type=Type('phene'), name='marker')])
], parse('featA:{featB}>>featC::marker+'))
def test_parse_markers(self):
self.assertEqual([
Ins(Feature(name='geneA'),
markers=[Feature(variant='wild-type', type=Type('phene'), name='markerA')])
], parse('+geneA::markerA+'))
self.assertEqual([
Del(Feature(name='geneA'),
markers=[Feature(variant='wild-type', type=Type('phene'), name='markerA'),
Feature(variant='mutant', type=Type('phene'), name='markerB')])
], parse('-geneA::{markerA+ markerB-}'))
def test_sequence_variants(self):
self.assertEqual([
Ins(Feature(name='geneA', variant='c.123A>G, p.M12N, p.Gln5*, foo'))
], parse('+geneA(c.123A>G, p.M12N, p.Gln5*, foo)'))
def test_variable_variants(self):
self.assertEqual([
Ins(Feature(name='geneA', variant='c.123A>G, org.foo.fooBar=42.0, fooString="bar"'))
], parse('+geneA(c.123A>G, org.foo.fooBar=42.0, fooString="bar")'))