def test_can_insert_then_insert_and_get_second_insert_only_as_changes(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
g1 = genome
# insert
g_u = g1.update()
with g_u.update_fragment_by_name("chrI") as f:
f.insert_bases(3, "gataca")
g2 = g_u
# insert again
g_u = g2.update()
with g_u.update_fragment_by_name("chrI") as f:
f.insert_bases(9, "gataca")
g3 = g_u
changes = g2.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertCountEqual(
[c.location for c in changes], [(1, 2), (3, 8), (9, len(s) + 6)]
)
changes = g3.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertCountEqual(
[c.location for c in changes], [(3, 8), (9, 14), (15, len(s) + 6 + 6)]
)
def test_find_annotation_by_qualifier(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f = genome.add_fragment('chrI', s)
f.annotate(3,
8,
'Foo gene',
'gene',
1,
qualifiers=dict(foo='bar,baz', far='foo,fu'))
# finds bar
annotations = genome.indexed_genome().find_annotation_by_qualifier(
'bar')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_qualifier(
'bAr')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# does not find bar,b
annotations = genome.indexed_genome().find_annotation_by_qualifier(
'bar,b')
self.assertEquals(len(annotations), 0)
# can limit to a field
annotations = genome.indexed_genome().find_annotation_by_qualifier(
'bar', fields=['foo'])
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# bar in qualifier, but not in 'far' field
annotations = genome.indexed_genome().find_annotation_by_qualifier(
'bar', fields=['far'])
self.assertEquals(len(annotations), 0)
# can search in multiple fields
annotations = \
genome.indexed_genome().find_annotation_by_qualifier('bar', fields=['far', 'foo'])
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
def setUp(self):
self.sequence = "agttcgaggctga"
self.genome = Genome.create("Foo")
self.fragment = Fragment.create_with_sequence("Bar", self.sequence)
Genome_Fragment(genome=self.genome,
fragment=self.fragment,
inherited=False).save()
def test_can_insert_then_insert_and_get_second_insert_only_as_changes(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
g1 = genome
# insert
g_u = g1.update()
with g_u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
g2 = g_u
# insert again
g_u = g2.update()
with g_u.update_fragment_by_name('chrI') as f:
f.insert_bases(9, 'gataca')
g3 = g_u
changes = g2.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertItemsEqual([c.location for c in changes], [(1, 2), (3, 8), (9, len(s) + 6)])
changes = g3.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertItemsEqual([c.location for c in changes], [
(3, 8), (9, 14), (15, len(s) + 6 + 6)])
def test_find_annotation_by_name(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f = genome.add_fragment('chrI', s)
f.annotate(3, 8, 'Foo gene', 'gene', 1)
annotations = genome.indexed_genome().find_annotation_by_name('Foo gene')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_name('foo gene')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
annotations = genome.indexed_genome().find_annotation_by_name('Foo bar')
self.assertEquals(len(annotations), 0)
def test_find_annotation_by_name(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f = genome.add_fragment('chrI', s)
f.annotate(3, 8, 'Foo gene', 'gene', 1)
annotations = genome.indexed_genome().find_annotation_by_name(
'Foo gene')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_name(
'foo gene')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
annotations = genome.indexed_genome().find_annotation_by_name(
'Foo bar')
self.assertEquals(len(annotations), 0)
def test_find_annotation_by_name(self):
genome = Genome.create("Foo")
s = "atggcatattcgcagct"
f = genome.add_fragment("chrI", s)
f.annotate(3, 8, "Foo gene", "gene", 1)
annotations = genome.indexed_genome().find_annotation_by_name("Foo gene")
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_name("foo gene")
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
annotations = genome.indexed_genome().find_annotation_by_name("Foo bar")
self.assertEquals(len(annotations), 0)
def on_post(self, request):
genome_parser = RequestParser()
genome_parser.add_argument('name', field_type=str, required=True, location='json')
genome_parser.add_argument('notes', field_type=str, location='json')
args = genome_parser.parse_args(request)
genome = Genome.create(name=args['name'], notes=args['notes'])
return GenomeView.to_dict(genome), 201
def test_add_fragments_to_genome_in_place(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
self.assertEquals(len(genome.fragments.all()), 1)
self.assertEquals(genome.fragments.all()[0].name, 'chrI')
self.assertEquals(genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_add_fragments_to_genome_in_place(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
self.assertEquals(len(genome.fragments.all()), 1)
self.assertEquals(genome.fragments.all()[0].name, "chrI")
self.assertEquals(genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_user_defined_fragments_does_not_include_genomic_fragment(self):
genome = Genome.create("Foo")
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
f = Fragment.create_with_sequence("Bar", "aacctaaaattataa")
self.assertEquals(len(Fragment.user_defined_fragments()), 1)
self.assertEquals(Fragment.user_defined_fragments()[0].name, "Bar")
self.assertEquals(Fragment.user_defined_fragments()[0].id, f.id)
def test_user_defined_fragments_does_not_include_genomic_fragment(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
f = Fragment.create_with_sequence('Bar', 'aacctaaaattataa')
self.assertEquals(len(Fragment.user_defined_fragments()), 1)
self.assertEquals(Fragment.user_defined_fragments()[0].name, 'Bar')
self.assertEquals(Fragment.user_defined_fragments()[0].id, f.id)
def test_add_fragments_to_genome_in_place(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
self.assertEquals(len(genome.fragments.all()), 1)
self.assertEquals(genome.fragments.all()[0].name, 'chrI')
self.assertEquals(
genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_user_defined_fragments_does_not_include_genomic_fragment(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
f = Fragment.create_with_sequence('Bar', 'aacctaaaattataa')
self.assertEquals(len(Fragment.user_defined_fragments()), 1)
self.assertEquals(Fragment.user_defined_fragments()[0].name, 'Bar')
self.assertEquals(Fragment.user_defined_fragments()[0].id, f.id)
def test_find_annotation_by_qualifier(self):
genome = Genome.create("Foo")
s = "atggcatattcgcagct"
f = genome.add_fragment("chrI", s)
f.annotate(
3, 8, "Foo gene", "gene", 1, qualifiers=dict(foo="bar,baz", far="foo,fu")
)
# finds bar
annotations = genome.indexed_genome().find_annotation_by_qualifier("bar")
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_qualifier("bAr")
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
# does not find bar,b
annotations = genome.indexed_genome().find_annotation_by_qualifier("bar,b")
self.assertEquals(len(annotations), 0)
# can limit to a field
annotations = genome.indexed_genome().find_annotation_by_qualifier(
"bar", fields=["foo"]
)
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
# bar in qualifier, but not in 'far' field
annotations = genome.indexed_genome().find_annotation_by_qualifier(
"bar", fields=["far"]
)
self.assertEquals(len(annotations), 0)
# can search in multiple fields
annotations = genome.indexed_genome().find_annotation_by_qualifier(
"bar", fields=["far", "foo"]
)
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, "Foo gene")
def test_get_changed_locations_by_fragment(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
s0 = "atggcatattcgcagct"
s1 = "gtacggctagtcgatt"
s2 = "acgatcgggattgagtcgattc"
# add initial sequence
f1 = genome.add_fragment("chrI", s0 + s1 + s2)
f2 = genome.add_fragment("chrII", s0 + s1 + s2)
# annotate it to break it up into chunks
with genome.annotate_fragment_by_name("chrI") as f:
f.annotate(1, len(s0), "F1", "feature", 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), "F2", "feature", 1)
f.annotate(
len(s0) + len(s1) + 1, len(s0) + len(s1) + len(s2), "F3", "feature", 1
)
with genome.annotate_fragment_by_name("chrII") as f:
f.annotate(1, len(s0), "F1", "feature", 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), "F2", "feature", 1)
f.annotate(
len(s0) + len(s1) + 1, len(s0) + len(s1) + len(s2), "F3", "feature", 1
)
# insert
u = genome.update()
with u.update_fragment_by_name("chrI") as f:
f.insert_bases(3, "gataca")
f1 = f
with u.update_fragment_by_name("chrII") as f:
f.insert_bases(3, "gataca")
f.insert_bases(6 + len(s0) + len(s1) + 2, "gataca")
f2 = f
g2 = Genome.objects.get(pk=u.pk)
changes = g2.indexed_genome().changed_locations_by_fragment()
for f in changes:
if f.id == f1.id:
self.assertEquals(changes[f], [[1, len(s0) + 6]])
elif f.id == f2.id:
self.assertEquals(
changes[f],
[
[1, len(s0) + 6],
[
len(s0) + len(s1) + 6 + 1,
len(s0) + 6 + len(s1) + len(s2) + 6,
],
],
)
else:
raise Exception("Unexpected fragment")
def on_post(self, request):
genome_parser = RequestParser()
genome_parser.add_argument('name',
field_type=str,
required=True,
location='json')
genome_parser.add_argument('notes', field_type=str, location='json')
args = genome_parser.parse_args(request)
genome = Genome.create(name=args['name'], notes=args['notes'])
return GenomeView.to_dict(genome), 201
def test_can_update_fragment_by_id_and_assign_new_name(self):
genome = Genome.create("Foo")
f0 = genome.add_fragment("chrI", "atggcatattcgcagct")
self.assertCountEqual([f.name for f in genome.fragments.all()], ["chrI"])
# insert
g = genome.update()
with g.update_fragment_by_fragment_id(f0.id, "foobar") as f:
f.insert_bases(3, "gataca")
self.assertCountEqual([fr.name for fr in g.fragments.all()], ["foobar"])
def test_can_update_fragment_by_id_and_assign_new_name(self):
genome = Genome.create('Foo')
f0 = genome.add_fragment('chrI', 'atggcatattcgcagct')
self.assertItemsEqual([f.name for f in genome.fragments.all()], ['chrI'])
# insert
g = genome.update()
with g.update_fragment_by_fragment_id(f0.id, 'foobar') as f:
f.insert_bases(3, 'gataca')
self.assertItemsEqual([fr.name for fr in g.fragments.all()], ['foobar'])
def on_post(self, request):
genome_parser = RequestParser()
genome_parser.add_argument("name",
field_type=str,
required=True,
location="json")
genome_parser.add_argument("notes", field_type=str, location="json")
args = genome_parser.parse_args(request)
genome = Genome.create(name=args["name"], notes=args["notes"])
return GenomeView.to_dict(genome), 201
def test_update_fragment_by_id(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f1 = genome.add_fragment('chrI', s)
g2 = genome.update()
with g2.update_fragment_by_fragment_id(f1.id) as f2:
f2.insert_bases(3, 'gataca')
self.assertEquals(g2.fragments.all()[0].indexed_fragment(
).sequence, s[0:2] + 'gataca' + s[2:])
self.assertEquals(genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_update_fragment_by_id(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f1 = genome.add_fragment('chrI', s)
g2 = genome.update()
with g2.update_fragment_by_fragment_id(f1.id) as f2:
f2.insert_bases(3, 'gataca')
self.assertEquals(g2.fragments.all()[0].indexed_fragment().sequence,
s[0:2] + 'gataca' + s[2:])
self.assertEquals(
genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_update_fragment_by_id(self):
genome = Genome.create("Foo")
s = "atggcatattcgcagct"
f1 = genome.add_fragment("chrI", s)
g2 = genome.update()
with g2.update_fragment_by_fragment_id(f1.id) as f2:
f2.insert_bases(3, "gataca")
self.assertEquals(
g2.fragments.all()[0].indexed_fragment().sequence, s[0:2] + "gataca" + s[2:]
)
self.assertEquals(genome.fragments.all()[0].indexed_fragment().sequence, s)
def test_can_update_fragment_by_id_and_assign_new_name(self):
genome = Genome.create('Foo')
f0 = genome.add_fragment('chrI', 'atggcatattcgcagct')
self.assertItemsEqual([f.name for f in genome.fragments.all()],
['chrI'])
# insert
g = genome.update()
with g.update_fragment_by_fragment_id(f0.id, 'foobar') as f:
f.insert_bases(3, 'gataca')
self.assertItemsEqual([fr.name for fr in g.fragments.all()],
['foobar'])
def test_get_changed_locations_by_fragment(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
s0 = 'atggcatattcgcagct'
s1 = 'gtacggctagtcgatt'
s2 = 'acgatcgggattgagtcgattc'
# add initial sequence
f1 = genome.add_fragment('chrI', s0 + s1 + s2)
f2 = genome.add_fragment('chrII', s0 + s1 + s2)
# annotate it to break it up into chunks
with genome.annotate_fragment_by_name('chrI') as f:
f.annotate(1, len(s0), 'F1', 'feature', 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), 'F2', 'feature', 1)
f.annotate(
len(s0) + len(s1) + 1,
len(s0) + len(s1) + len(s2), 'F3', 'feature', 1)
with genome.annotate_fragment_by_name('chrII') as f:
f.annotate(1, len(s0), 'F1', 'feature', 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), 'F2', 'feature', 1)
f.annotate(
len(s0) + len(s1) + 1,
len(s0) + len(s1) + len(s2), 'F3', 'feature', 1)
# insert
u = genome.update()
with u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
f1 = f
with u.update_fragment_by_name('chrII') as f:
f.insert_bases(3, 'gataca')
f.insert_bases(6 + len(s0) + len(s1) + 2, 'gataca')
f2 = f
g2 = Genome.objects.get(pk=u.pk)
changes = g2.indexed_genome().changed_locations_by_fragment()
for f in changes:
if f.id == f1.id:
self.assertEquals(changes[f], [[1, len(s0) + 6]])
elif f.id == f2.id:
self.assertEquals(changes[f],
[[1, len(s0) + 6],
[
len(s0) + len(s1) + 6 + 1,
len(s0) + 6 + len(s1) + len(s2) + 6
]])
else:
raise Exception('Unexpected fragment')
def test_can_set_name_on_update(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
# insert
u = genome.update(name=u'Bar bar')
with u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
u = Genome.objects.get(pk=u.pk)
self.assertEquals(u.name, u'Bar bar')
def test_can_set_name_on_update(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
# insert
u = genome.update(name=u'Bar bar')
with u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
u = Genome.objects.get(pk=u.pk)
self.assertEquals(u.name, u'Bar bar')
def test_can_set_name_on_update(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
# insert
u = genome.update(name=u"Bar bar")
with u.update_fragment_by_name("chrI") as f:
f.insert_bases(3, "gataca")
u = Genome.objects.get(pk=u.pk)
self.assertEquals(u.name, u"Bar bar")
def test_find_annotation_by_qualifier(self):
genome = Genome.create('Foo')
s = 'atggcatattcgcagct'
f = genome.add_fragment('chrI', s)
f.annotate(3, 8, 'Foo gene', 'gene', 1, qualifiers=dict(foo='bar,baz', far='foo,fu'))
# finds bar
annotations = genome.indexed_genome().find_annotation_by_qualifier('bar')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# case insensitive
annotations = genome.indexed_genome().find_annotation_by_qualifier('bAr')
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# does not find bar,b
annotations = genome.indexed_genome().find_annotation_by_qualifier('bar,b')
self.assertEquals(len(annotations), 0)
# can limit to a field
annotations = genome.indexed_genome().find_annotation_by_qualifier('bar', fields=['foo'])
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
# bar in qualifier, but not in 'far' field
annotations = genome.indexed_genome().find_annotation_by_qualifier('bar', fields=['far'])
self.assertEquals(len(annotations), 0)
# can search in multiple fields
annotations = \
genome.indexed_genome().find_annotation_by_qualifier('bar', fields=['far', 'foo'])
self.assertEquals(len(annotations), 1)
self.assertEquals(f.id in annotations, True)
self.assertEquals(len(annotations[f.id]), 1)
self.assertEquals(annotations[f.id][0].base_first, 3)
self.assertEquals(annotations[f.id][0].base_last, 8)
self.assertEquals(annotations[f.id][0].feature.name, 'Foo gene')
def test_add_fragments_to_genome_not_in_place_creates_and_updates_child(self):
parent = Genome.create('Foo')
self.assertEquals(len(Genome.objects.all()), 1)
u = parent.update()
s = 'atggcatattcgcagct'
u.add_fragment('chrI', s)
child = u
# created a child genome
self.assertItemsEqual([g.id for g in Genome.objects.all()], [parent.id, child.id])
# child genome points to parent genome
self.assertEquals(child.parent.id, parent.id)
# child genome has changes, parent does not
self.assertEquals(len(child.fragments.all()), 1)
self.assertEquals(len(parent.fragments.all()), 0)
def test_add_fragments_to_genome_not_in_place_creates_and_updates_child(self):
parent = Genome.create("Foo")
self.assertEquals(len(Genome.objects.all()), 1)
u = parent.update()
s = "atggcatattcgcagct"
u.add_fragment("chrI", s)
child = u
# created a child genome
self.assertCountEqual(
[g.id for g in Genome.objects.all()], [parent.id, child.id]
)
# child genome points to parent genome
self.assertEquals(child.parent.id, parent.id)
# child genome has changes, parent does not
self.assertEquals(len(child.fragments.all()), 1)
self.assertEquals(len(parent.fragments.all()), 0)
def test_can_insert_and_get_changes(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
# insert
g_u = genome.update()
with g_u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
g = g_u
changes = g.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertItemsEqual([c.location for c in changes], [(1, 2), (3, 8), (9, len(s) + 6)])
def test_get_changed_locations_by_fragment(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
s0 = 'atggcatattcgcagct'
s1 = 'gtacggctagtcgatt'
s2 = 'acgatcgggattgagtcgattc'
# add initial sequence
f1 = genome.add_fragment('chrI', s0 + s1 + s2)
f2 = genome.add_fragment('chrII', s0 + s1 + s2)
# annotate it to break it up into chunks
with genome.annotate_fragment_by_name('chrI') as f:
f.annotate(1, len(s0), 'F1', 'feature', 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), 'F2', 'feature', 1)
f.annotate(len(s0) + len(s1) + 1, len(s0) + len(s1) + len(s2), 'F3', 'feature', 1)
with genome.annotate_fragment_by_name('chrII') as f:
f.annotate(1, len(s0), 'F1', 'feature', 1)
f.annotate(len(s0) + 1, len(s0) + len(s1), 'F2', 'feature', 1)
f.annotate(len(s0) + len(s1) + 1, len(s0) + len(s1) + len(s2), 'F3', 'feature', 1)
# insert
u = genome.update()
with u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
f1 = f
with u.update_fragment_by_name('chrII') as f:
f.insert_bases(3, 'gataca')
f.insert_bases(6 + len(s0) + len(s1) + 2, 'gataca')
f2 = f
g2 = Genome.objects.get(pk=u.pk)
changes = g2.indexed_genome().changed_locations_by_fragment()
for f in changes:
if f.id == f1.id:
self.assertEquals(changes[f], [[1, len(s0) + 6]])
elif f.id == f2.id:
self.assertEquals(
changes[f],
[[1, len(s0) + 6],
[len(s0) + len(s1) + 6 + 1, len(s0) + 6 + len(s1) + len(s2) + 6]])
else:
raise Exception('Unexpected fragment')
def test_can_remove_and_get_changes_back(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
g = genome
# remove
g_u = g.update()
with g_u.update_fragment_by_name('chrI') as f:
f.remove_bases(3, 4)
g = g_u
changes = g.indexed_genome().changes()
self.assertEquals(len(changes), 2)
self.assertItemsEqual([c.location for c in changes], [(1, 2), (3, len(s) - 4)])
def test_can_remove_and_get_changes_back(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
g = genome
# remove
g_u = g.update()
with g_u.update_fragment_by_name("chrI") as f:
f.remove_bases(3, 4)
g = g_u
changes = g.indexed_genome().changes()
self.assertEquals(len(changes), 2)
self.assertCountEqual([c.location for c in changes], [(1, 2), (3, len(s) - 4)])
def test_can_insert_and_get_changes(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
# insert
g_u = genome.update()
with g_u.update_fragment_by_name('chrI') as f:
f.insert_bases(3, 'gataca')
g = g_u
changes = g.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertItemsEqual([c.location for c in changes], [(1, 2), (3, 8),
(9, len(s) + 6)])
def test_can_insert_and_get_changes(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
# add initial sequence
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
# insert
g_u = genome.update()
with g_u.update_fragment_by_name("chrI") as f:
f.insert_bases(3, "gataca")
g = g_u
changes = g.indexed_genome().changes()
self.assertEquals(len(changes), 3)
self.assertCountEqual(
[c.location for c in changes], [(1, 2), (3, 8), (9, len(s) + 6)]
)
def setUp(self):
self.genome = Genome.create("Test")
self.root_sequence = "agttcgaggctga"
self.root = Fragment.create_with_sequence("Foo", self.root_sequence)
def setUp(self):
self.genome = Genome.create('Test')
self.root_sequence = 'agttcgaggctga'
self.root = Fragment.create_with_sequence('Foo', self.root_sequence)
def test_changes_return_empty_array_if_no_parent(self):
genome = Genome.create('Foo')
self.assertEquals(len(genome.fragments.all()), 0)
s = 'atggcatattcgcagct'
genome.add_fragment('chrI', s)
self.assertEquals(genome.indexed_genome().changes(), [])
def test_create_genome(self):
self.assertEquals(len(Genome.objects.all()), 0)
genome = Genome.create('Foo')
self.assertEquals(len(Genome.objects.all()), 1)
self.assertEquals(Genome.objects.all()[0].name, 'Foo')
self.assertEquals(Genome.objects.all()[0].id, genome.id)
def test_changes_return_empty_array_if_no_parent(self):
genome = Genome.create("Foo")
self.assertEquals(len(genome.fragments.all()), 0)
s = "atggcatattcgcagct"
genome.add_fragment("chrI", s)
self.assertEquals(genome.indexed_genome().changes(), [])
#
# Example:
# python split_gff.py GRCh38 GRCh38_latest_genomic.gff GRCh38_latest_genomic.fna
# in docker, run
# time scripts/_python example/import_multi.py 'GRCh38.2' example/GRCh38/*combined.gff
# time scripts/_python example/import_multi.py GCA_003668045.2 example/GCA_003668045.2/*combined.gff
import django
django.setup()
import sys
from edge.models import Genome
from edge.importer import GFFImporter
name = sys.argv[1]
fns = sys.argv[2:]
"""
if Genome.objects.filter(name=name).count() > 0:
raise Exception('There is already a genome named "%s"' % (name,))
"""
if Genome.objects.filter(name=name).count() > 0:
genome = Genome.objects.get(name=name)
else:
genome = Genome.create(name)
for gff_fasta_fn in fns:
print(gff_fasta_fn)
GFFImporter(genome, gff_fasta_fn).do_import()
def test_create_genome(self):
self.assertEquals(len(Genome.objects.all()), 0)
genome = Genome.create("Foo")
self.assertEquals(len(Genome.objects.all()), 1)
self.assertEquals(Genome.objects.all()[0].name, "Foo")
self.assertEquals(Genome.objects.all()[0].id, genome.id)
