def setUp(self):
import os
import tempfile
from edge import import_gff
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()
import_gff('TestGenome', f.name)
self.genome = Genome.objects.get(name='TestGenome')
os.unlink(f.name)
self.assertItemsEqual([f.name for f in self.genome.fragments.all()], ['chrI', 'chrII'])
def test_import_gff_procedure_creates_genome_and_annotations(self):
from edge import import_gff
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()
self.assertEquals(
Genome.objects.filter(name='TestGenome').count(), 0)
import_gff('TestGenome', f.name)
self.assertEquals(
Genome.objects.filter(name='TestGenome').count(), 1)
# import again with same name does not work
self.assertRaises(Exception, import_gff, 'TestGenome', f.name)
# can import again with different name
self.assertEquals(
Genome.objects.filter(name='TestGenome2').count(), 0)
import_gff('TestGenome2', f.name)
self.assertEquals(
Genome.objects.filter(name='TestGenome2').count(), 1)
genome = Genome.objects.get(name='TestGenome')
os.unlink(f.name)
# created one fragment for each sequence in GFF file
self.assertItemsEqual([f.name for f in genome.fragments.all()],
['chrI', 'chrII'])
chrI = [
f.indexed_fragment() for f in genome.fragments.all()
if f.name == 'chrI'
][0]
self.assertEquals(len(chrI.sequence), 160)
self.assertEquals(len(chrI.annotations()), 2)
chrII = [
f.indexed_fragment() for f in genome.fragments.all()
if f.name == 'chrII'
][0]
self.assertEquals(len(chrII.sequence), 160)
self.assertEquals(len(chrII.annotations()), 2)
def test_import_gff_procedure_creates_genome_and_annotations(self):
from edge import import_gff
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()
self.assertEquals(Genome.objects.filter(name='TestGenome').count(), 0)
import_gff('TestGenome', f.name)
self.assertEquals(Genome.objects.filter(name='TestGenome').count(), 1)
# import again with same name does not work
self.assertRaises(Exception, import_gff, 'TestGenome', f.name)
# can import again with different name
self.assertEquals(Genome.objects.filter(name='TestGenome2').count(), 0)
import_gff('TestGenome2', f.name)
self.assertEquals(Genome.objects.filter(name='TestGenome2').count(), 1)
genome = Genome.objects.get(name='TestGenome')
os.unlink(f.name)
# created one fragment for each sequence in GFF file
self.assertItemsEqual([f.name for f in genome.fragments.all()], ['chrI', 'chrII'])
chrI = [f.indexed_fragment() for f in genome.fragments.all() if f.name == 'chrI'][0]
self.assertEquals(len(chrI.sequence), 160)
self.assertEquals(len(chrI.annotations()), 2)
chrII = [f.indexed_fragment() for f in genome.fragments.all() if f.name == 'chrII'][0]
self.assertEquals(len(chrII.sequence), 160)
self.assertEquals(len(chrII.annotations()), 2)
def genome_import(request):
res = {
'imported_genomes': [],
}
for name in request.FILES:
with tempfile.NamedTemporaryFile(mode='rw+b', delete=False) as gff:
for chuck in request.FILES.get(name).chunks():
gff.write(chuck)
g = import_gff(name, gff.name)
os.unlink(gff.name)
blastdb_task = build_genome_blastdb.delay(g.id)
res['imported_genomes'].append({
'id': g.id,
'name': g.name,
'blastdb_task_id': blastdb_task.id,
})
return JsonResponse(res)
def genome_import(request):
res = {
"imported_genomes": [],
}
for name in request.FILES:
with tempfile.NamedTemporaryFile(mode="w+b", delete=False) as gff:
for chuck in request.FILES.get(name).chunks():
gff.write(chuck)
g = import_gff(name, gff.name)
os.unlink(gff.name)
blastdb_task = build_genome_blastdb.delay(g.id)
res["imported_genomes"].append({
"id": g.id,
"name": g.name,
"blastdb_task_id": blastdb_task.id,
})
return JsonResponse(res)
# flake8: noqa import django django.setup() import sys from edge import import_gff import_gff(sys.argv[1], sys.argv[2])
def handle(self, *args, **options):
if len(args) != 2:
raise Exception("Expecting two arguments: name of genome and GFF file")
import_gff(args[0], args[1])
def handle(self, *args, **options):
if len(args) != 2:
raise Exception('Expecting two arguments: name of genome and GFF file')
import_gff(args[0], args[1])