def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name="Foo")
a.save()
Genome(name="Bar %s" % a.id).save()
# no filter, return both genomes
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo", "Bar %s" % a.id])
# finds genome by ID and query
res = self.client.get("%s?q=%s" % (url, a.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo", "Bar %s" % a.id])
# finds one
res = self.client.get("%s?q=oo" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], ["Foo"])
# finds none
res = self.client.get("%s?q=ooo" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["name"] for g in d], [])
def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement()) + "tttttttttt"
res = self.client.post(
"/edge/genomes/%s/blast/" % g1.id,
data=json.dumps(dict(program="blastn", query=query)),
content_type="application/json",
)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]["fragment_id"], f1.id)
self.assertEquals(d[0]["query_start"], 1)
self.assertEquals(d[0]["query_end"], 14)
self.assertEquals(d[0]["subject_start"], 20)
self.assertEquals(d[0]["subject_end"], 7)
def test_genome_list_paginates(self):
from edge.models import Genome
Genome(name="Foo").save()
Genome(name="Bar").save()
Genome(name="Far").save()
Genome(name="Baz").save()
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 4)
res = self.client.get("%s?s=1" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 3)
res = self.client.get("%s?s=1&p=2" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
res = self.client.get("%s?p=2" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
def test_genome_list_paginates(self):
from edge.models import Genome
Genome(name='Foo').save()
Genome(name='Bar').save()
Genome(name='Far').save()
Genome(name='Baz').save()
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 4)
res = self.client.get('/edge/genomes/?s=1')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 3)
res = self.client.get('/edge/genomes/?s=1&p=2')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
res = self.client.get('/edge/genomes/?p=2')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name='Foo')
a.save()
Genome(name='Bar %s' % a.id).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds genome by ID and query
res = self.client.get('/edge/genomes/?q=%s' % a.id)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds one
res = self.client.get('/edge/genomes/?q=oo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo'])
# finds none
res = self.client.get('/edge/genomes/?q=ooo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], [])
def test_finds_genomes_with_name(self):
from edge.models import Genome
a = Genome(name='Foo')
a.save()
Genome(name='Bar %s' % a.id).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds genome by ID and query
res = self.client.get('/edge/genomes/?q=%s' % a.id)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])
# finds one
res = self.client.get('/edge/genomes/?q=oo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], ['Foo'])
# finds none
res = self.client.get('/edge/genomes/?q=ooo')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['name'] for g in d], [])
def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(
dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 20)
self.assertEquals(d[0]['subject_end'], 7)
def test_blast_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
query = str(Seq(s1[6:20]).reverse_complement())+'tttttttttt'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 20)
self.assertEquals(d[0]['subject_end'], 7)
def build_genome(self, circular, *templates):
g = Genome(name='Foo')
g.save()
for seq in templates:
f = Fragment.create_with_sequence('Bar', seq, circular=circular)
Genome_Fragment(genome=g, fragment=f, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f))
except:
pass
build_all_genome_dbs(refresh=True)
return Genome.objects.get(pk=g.id)
def test_finds_sequence_on_specified_genome(self):
s1 = get_random_sequence(200)
s2 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
f2 = Fragment.create_with_sequence("Baz", s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name="Far")
g2.save()
f3 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + "aaaaaaaaa"
r = blast_genome(g1, "blastn", query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def test_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + 'aaaaaaaaa'
r = blast_genome(g1, 'blastn', query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def test_does_not_return_genomic_fragments(self):
from edge.models import Genome, Genome_Fragment
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 1)
g = Genome(name='Foo')
g.save()
Genome_Fragment(genome=g, fragment_id=self.fragment_id, inherited=False).save()
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 0)
def test_builds_genome_db_with_different_names_on_separate_attempts(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
dbname1 = build_genome_db(g1)
self.assertEquals(dbname1 is None, False)
self.assertEquals(dbname1, g1.blastdb)
g1.blastdb = None
dbname2 = build_genome_db(g1)
self.assertEquals(dbname2 == dbname1, False)
def build_genome_and_ancestors(self, names):
# build a genome of name in names with each as its subsquent genome's parent
g_parent = Genome(name=names[0])
g_parent.save()
g_child = g_parent
for name in names[:-1]:
g_child = Genome(name=name)
g_child.parent = g_parent
g_child.save()
g_parent = g_child
return g_child
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_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_import_feature_ending_at_last_base(self):
data = """##gff-version 3
chrI\tTest\tchromosome\t1\t160\t.\t.\t.\tID=i1;Name=f1
chrI\tTest\tcds\t20\t28\t.\t-\t.\tID=i2;Name=f2
chrI\tTest\trbs\t20\t160\t.\t+\t.\tID=i3
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
"""
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)
# verify chrI fragment
chrI = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrI'][0]
self.assertEquals(len(chrI.sequence), 160)
# verify skips annotation on entire sequence
self.assertEquals(len(chrI.annotations()), 2)
self.assertEquals(chrI.annotations()[1].base_first, 20)
self.assertEquals(chrI.annotations()[1].base_last, 160)
self.assertEquals(chrI.annotations()[1].feature.name, 'i3') # no name, loaded ID
self.assertEquals(chrI.annotations()[1].feature.strand, 1)
self.assertEquals(chrI.annotations()[0].base_first, 20)
self.assertEquals(chrI.annotations()[0].base_last, 28)
self.assertEquals(chrI.annotations()[0].feature.name, 'f2')
self.assertEquals(chrI.annotations()[0].feature.strand, -1)
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_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_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_genome_list_does_not_return_inactive_genomes(self):
from edge.models import Genome
Genome(name='Foo', active=False).save()
Genome(name='Bar', active=False).save()
Genome(name='Far').save()
Genome(name='Baz').save()
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
self.assertEqual('Foo' in res.content, False)
self.assertEqual('Bar' in res.content, False)
self.assertEqual('Far' in res.content, True)
self.assertEqual('Baz' in res.content, True)
def test_does_not_return_genomic_fragments(self):
from edge.models import Genome, Genome_Fragment
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 1)
g = Genome(name='Foo')
g.save()
Genome_Fragment(genome=g,
fragment_id=self.fragment_id,
inherited=False).save()
res = self.client.get('/edge/fragments/')
self.assertEquals(res.status_code, 200)
self.assertEquals(len(json.loads(res.content)), 0)
def test_builds_fragment_fastas(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
fn = fragment_fasta_fn(f1)
try:
os.unlink(fn)
except BaseException:
pass
fn = build_fragment_fasta(f1)
records = list(SeqIO.parse(fn, "fasta"))
self.assertEquals(len(records), 1)
self.assertEquals(str(records[0].seq), s1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
def test_does_not_return_duplicate_hits_for_circular_fragments(self):
s1 = get_random_sequence(200)
g1 = Genome(name="Foo")
g1.save()
f1 = Fragment.create_with_sequence("Bar", s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except BaseException:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[5:20] + "tttttttttt"
r = blast_genome(g1, "blastn", query)
self.assertEquals(len(r), 1)
def test_genome_list_does_not_return_inactive_genomes(self):
from edge.models import Genome
Genome(name="Foo", active=False).save()
Genome(name="Bar", active=False).save()
Genome(name="Far").save()
Genome(name="Baz").save()
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEqual(len(d), 2)
self.assertEqual(b"Foo" in res.content, False)
self.assertEqual(b"Bar" in res.content, False)
self.assertEqual(b"Far" in res.content, True)
self.assertEqual(b"Baz" in res.content, True)
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 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_finds_genomes_with_specified_fragment_ids(self):
g1 = Genome(name="Foo")
g1.save()
g2 = Genome(name="Bar")
g2.save()
f1 = Fragment(circular=True, name="FooF1")
f1.save()
f2 = Fragment(circular=True, name="FooF2")
f2.save()
f3 = Fragment(circular=True, name="FooF3", parent=f2)
f3.save()
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
# no filter, return both genomes
url = reverse("genome_list")
res = self.client.get(url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g1.id, g2.id])
# looking for f1 and f2
res = self.client.get("%s?f=%d&f=%d" % (url, f1.id, f2.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g1.id])
# looking for f1 and f3
res = self.client.get("%s?f=%d&f=%d" % (url, f1.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertCountEqual([g["id"] for g in d], [g2.id])
# looking for f2 and f3
res = self.client.get("%s?f=%d&f=%d" % (url, f2.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# looking for f1
res = self.client.get("%s?f=%d" % (
url,
f1.id,
))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# bad input, return []
res = self.client.get("%s?f=[1,2,3]" % url)
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
def test_derives_new_genome_with_multiple_fragments(self):
g1 = Genome(name="Foo")
g1.save()
url = reverse("derive-genome-with-new-fragments",
kwargs={"genome_id": g1.id})
res = self.client.post(
url,
data=json.dumps([
{
"name": "test-fragment",
"sequence": "AGCTAGCTTCGATCGA"
},
{
"name": "circular-fragment",
"sequence": "AGCTAGCTTCGATCGAAGCTATTATATCGATA",
"circular": True,
},
]),
content_type="application/json",
)
self.assertEquals(res.status_code, 201)
child = Genome.objects.get(parent=g1.id)
self.assertNotEquals(child.id, g1.id)
fragments = [{
"id": fragment.id,
"uri": "/edge/fragments/{}/".format(fragment.id),
"name": fragment.name,
"circular": fragment.circular,
"parent_id": None,
"length": fragment.indexed_fragment().length,
} for fragment in child.fragments.all()]
self.assertEquals(
json.loads(res.content),
{
"fragments": fragments,
"id": child.id,
"name": child.name,
"notes": None,
"parent_id": g1.id,
"parent_name": g1.name,
"uri": "/edge/genomes/{}/".format(child.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_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_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_derives_new_genome_after_adding_fragment(self):
g1 = Genome(name="Foo")
g1.save()
url = reverse("derive-genome-with-new-fragments",
kwargs={"genome_id": g1.id})
res = self.client.post(
url,
data=json.dumps([{
"name": "test-fragment",
"sequence": "AGCTAGCTTCGATCGA"
}]),
content_type="application/json",
)
self.assertEquals(res.status_code, 201)
child = Genome.objects.get(parent=g1.id)
self.assertNotEquals(child.id, g1.id)
fragment = child.fragments.first()
self.assertEquals(
json.loads(res.content),
{
"fragments": [{
"id": fragment.id,
"uri": "/edge/fragments/{}/".format(fragment.id),
"name": fragment.name,
"circular": fragment.circular,
"parent_id": None,
"length": 16,
}],
"id":
child.id,
"name":
child.name,
"notes":
None,
"parent_id":
g1.id,
"parent_name":
g1.name,
"uri":
"/edge/genomes/{}/".format(child.id),
},
)
def test_does_not_align_sequence_across_boundry_for_non_circular_fragment(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=False)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + 'tttttttttt'
res = blast_genome(g1, 'blastn', query)
for r in res:
self.assertEquals(r.subject_start > 0 and r.subject_start <= len(s1), True)
self.assertEquals(r.subject_end > 0 and r.subject_end <= len(s1), True)
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_import_gff_creates_fragments_and_annotate_features(self):
data = """##gff-version 3
chrI\tTest\tchromosome\t1\t160\t.\t.\t.\tID=i1;Name=f1
chrI\tTest\tcds\t30\t80\t.\t-\t.\tID=i2;Name=f2
chrI\tTest\trbs\t20\t28\t.\t+\t.\tID=i3
chrII\tTest\tgene\t40\t60\t.\t-\t.\tID=f4;gene=g4
chrII\tTest\tgene\t20\t80\t.\t+\t.\tID=i5;Name=f5
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
>chrII
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
"""
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)
# created one fragment for each sequence in GFF file
self.assertItemsEqual([fr.name for fr in genome.fragments.all()], ['chrI', 'chrII'])
# verify chrI fragment
chrI = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrI'][0]
self.assertEquals(len(chrI.sequence), 160)
# verify skips annotation on entire sequence
self.assertEquals(len(chrI.annotations()), 2)
self.assertEquals(chrI.annotations()[0].base_first, 20)
self.assertEquals(chrI.annotations()[0].base_last, 28)
self.assertEquals(chrI.annotations()[0].feature.name, 'i3') # no name, loaded ID
self.assertEquals(chrI.annotations()[0].feature.strand, 1)
self.assertEquals(chrI.annotations()[1].base_first, 30)
self.assertEquals(chrI.annotations()[1].base_last, 80)
self.assertEquals(chrI.annotations()[1].feature.name, 'f2')
self.assertEquals(chrI.annotations()[1].feature.strand, -1)
# verify chrII fragment
chrII = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrII'][0]
self.assertEquals(len(chrII.sequence), 160)
# consecutive annotations merged even though they span multiple chunks
self.assertEquals(len(chrII.annotations()), 2)
self.assertEquals(chrII.annotations()[0].base_first, 20)
self.assertEquals(chrII.annotations()[0].base_last, 80)
self.assertEquals(chrII.annotations()[0].feature.name, 'f5')
self.assertEquals(chrII.annotations()[0].feature.strand, 1)
self.assertEquals(chrII.annotations()[1].base_first, 40)
self.assertEquals(chrII.annotations()[1].base_last, 60)
self.assertEquals(chrII.annotations()[1].feature.name, 'g4') # has gene, use gene name
self.assertEquals(chrII.annotations()[1].feature.strand, -1)
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_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = s1[6:20] + 'aaaaaaaaa'
r = blast_genome(g1, 'blastn', query)
# only returns hit from genome
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 7)
self.assertEquals(r[0].subject_end, 20)
self.assertEquals(r[0].strand(), 1)
def import_gff(name, fn):
"""
Creates a new genome using the specified GFF file.
name: Name of genome
fn: path to GFF file
"""
from edge.models import Genome
if Genome.objects.filter(name=name).count() > 0:
raise Exception('There is already a genome named "%s"' % (name,))
g = Genome.import_gff(name, fn)
return g
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_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_aligns_sequence_to_antisense_strand(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
r = blast_genome(g1, 'blastn', query)
self.assertEquals(len(r), 1)
self.assertEquals(r[0].fragment_id, f1.id)
self.assertEquals(r[0].query_start, 1)
self.assertEquals(r[0].query_end, 14)
self.assertEquals(r[0].subject_start, 20)
self.assertEquals(r[0].subject_end, 7)
self.assertEquals(r[0].strand(), -1)
def import_with_qualifiers(self, qualifiers):
data = """##gff-version 3
chrI\tTest\tcds\t30\t80\t.\t-\t.\t%s
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
""" % (qualifiers,)
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
self.genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)
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_aligns_sequence_across_boundry_for_circular_fragment(self):
s1 = 'atcggtatctactatgcgtatgcgtcatgattatatatattagcggcatg'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
except:
pass
build_all_genome_dbs(refresh=True)
g1 = Genome.objects.get(pk=g1.id)
query = (s1[-10:] + s1[0:10]) + 'ttttttttttt'
res = blast_genome(g1, 'blastn', query)
# we are not removing redundant matches when matching across circular
# boundaries, since blasting across circular boundary of a genome is a
# rare case. so in this particular case, you will find two results, one
# for the end of the query at the start of the genome, one for across
# the circular boundary.
found = False
for r in res:
if r.query_start == 1 and r.query_end == 20:
self.assertEquals(r.fragment_id, f1.id)
self.assertEquals(r.query_start, 1)
self.assertEquals(r.query_end, 20)
self.assertEquals(r.subject_start, len(s1) - 10 + 1)
self.assertEquals(r.subject_end, len(s1) + 10)
self.assertEquals(r.fragment_length, len(s1))
self.assertEquals(r.strand(), 1)
found = True
break
self.assertEquals(found, True)
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_finds_genomes_with_specified_fragment_ids(self):
from edge.models import Genome, Fragment, Genome_Fragment
g1 = Genome(name='Foo')
g1.save()
g2 = Genome(name='Bar')
g2.save()
f1 = Fragment(circular=True, name='FooF1')
f1.save()
f2 = Fragment(circular=True, name='FooF2')
f2.save()
f3 = Fragment(circular=True, name='FooF3', parent=f2)
f3.save()
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
# no filter, return both genomes
res = self.client.get('/edge/genomes/')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id, g2.id])
# looking for f1 and f2
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f2.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g1.id])
# looking for f1 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertItemsEqual([g['id'] for g in d], [g2.id])
# looking for f2 and f3
res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f2.id, f3.id))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# looking for f1
res = self.client.get('/edge/genomes/?f=%d' % (f1.id,))
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
# bad input, return []
res = self.client.get('/edge/genomes/?f=[1,2,3]')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(d, [])
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_blast_finds_sequence_on_specified_genome(self):
s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
g1 = Genome(name='Foo')
g1.save()
f1 = Fragment.create_with_sequence('Bar', s1)
f2 = Fragment.create_with_sequence('Baz', s2)
Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
g2 = Genome(name='Far')
g2.save()
f3 = Fragment.create_with_sequence('Bar', s1)
Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()
try:
os.unlink(fragment_fasta_fn(f1))
os.unlink(fragment_fasta_fn(f2))
os.unlink(fragment_fasta_fn(f3))
except:
pass
build_all_genome_dbs(refresh=True)
query = s1[6:20]+'aaaaaaaaa'
res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
# only returns hit from genome
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f1.id)
self.assertEquals(d[0]['query_start'], 1)
self.assertEquals(d[0]['query_end'], 14)
self.assertEquals(d[0]['subject_start'], 7)
self.assertEquals(d[0]['subject_end'], 20)
# blast in other genome works too
res = self.client.post('/edge/genomes/%s/blast/' % g2.id,
data=json.dumps(dict(program='blastn', query=query)),
content_type='application/json')
self.assertEquals(res.status_code, 200)
d = json.loads(res.content)
self.assertEquals(len(d), 1)
self.assertEquals(d[0]['fragment_id'], f3.id)
def setUp(self):
self.genome = Genome.create('Test')
self.root_sequence = 'agttcgaggctga'
self.root = Fragment.create_with_sequence('Foo', self.root_sequence)
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)
