def test_autocomplete_name(self):
suggestions = LocationService(db='test').autocomplete_name("N")
self.assertEqual(suggestions, [
'NADK', 'NCLN', 'NCRNA00115', 'NET15', 'NET59', 'NET7', 'NICALIN',
'NIR', 'NOC2L', 'NPHP4'
])
suggestions = LocationService(db='test').autocomplete_name("NO")
self.assertEqual(suggestions, ['NOC2L'])
def test_parse_basic(self):
r = LocationService.parse_genomic_range("chr1:123-456")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 123)
self.assertEqual(r.end, 456)
r = LocationService.parse_genomic_range("chr1:0-800000")
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 0)
self.assertEqual(r.end, 800000)
def test_parse_basic(self):
r = LocationService.parse_genomic_range("chr1:123-456")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 123)
self.assertEqual(r.end, 456)
r = LocationService.parse_genomic_range("chr1:0-800000")
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 0)
self.assertEqual(r.end, 800000)
def test_find_gene(self):
rlist = LocationService(db='test').find(" NOC2L")
self.assertIsInstance(rlist, list)
self.assertEqual(len(rlist), 1)
r = rlist[0]
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 879584) # first snp occurrence
self.assertEqual(r.end, 894689) # last snp occurrence
def test_find_chrom_only(self):
rlist = LocationService(db='test').find(" chr1 ")
self.assertIsInstance(rlist, list)
self.assertEqual(len(rlist), 1)
r = rlist[0]
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start,
69510) # first snp occurrence (select all samples!)
self.assertEqual(r.end, 167385327) # last snp occurrence
def test_find_gene_2locs(self):
"""This gene is annotated on 2 chromosomes, thus appears at two different locations"""
rlist = LocationService(db='test').find("AGRN")
self.assertIsInstance(rlist, list)
self.assertEqual(len(rlist), 1)
r = rlist[0]
self.assertEqual(r.chrom, 'chr1')
self.assertEqual(r.start, 955503) # first snp occurrence
self.assertEqual(r.end, 991496) # last snp occurrence
def parse_arg(self, arg):
"""Return a list of `GenomicRange`s"""
return LocationService(db=self.db).find(arg)
def test_find_region(self):
rlist = LocationService(db='test').find("chrX:1-1000000")
self.assertEqual(len(rlist), 1)
def test_parse_with_spaces_after_dash(self):
r = LocationService.parse_genomic_range("chr1: 123,456,111- 123,456,987")
self.assertIsInstance(r, GenomicRange)
def test_parse_with_comma(self):
r = LocationService.parse_genomic_range("chr1:123,456,111-123,456,987")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chr1')
def test_parse_chrX(self):
r = LocationService.parse_genomic_range("chrX:123-456")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chrX')
self.assertEqual(r.start, 123)
self.assertEqual(r.end, 456)
def test_find_region_with_commas(self):
rlist = LocationService(db='test').find("chr1:955,503-955,503")
self.assertEqual(len(rlist), 1)
def test_find_multiple_genes(self):
rlist = LocationService(
db='test').find("AGRN, NOC2L,NIR ,NET7,IDONTEXIST")
self.assertEqual(len(rlist), 4)
def test_find_mix(self):
rlist = LocationService(db='test').find("AGRN,chr2")
self.assertEqual(len(rlist), 2)
def location_find(request, db, loc='', **kwargs):
"""Return an exposed GenomicRange for each location in the comma-separated list *loc*."""
locs = LocationService(db).find(loc)
locations = [l.expose() for l in locs]
return JsonResponse(locations, safe=False)
def test_parse_with_spaces_after_dash(self):
r = LocationService.parse_genomic_range(
"chr1: 123,456,111- 123,456,987")
self.assertIsInstance(r, GenomicRange)
def test_parse_with_comma(self):
r = LocationService.parse_genomic_range("chr1:123,456,111-123,456,987")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chr1')
def test_parse_chrX(self):
r = LocationService.parse_genomic_range("chrX:123-456")
self.assertIsInstance(r, GenomicRange)
self.assertEqual(r.chrom, 'chrX')
self.assertEqual(r.start, 123)
self.assertEqual(r.end, 456)
def test_find_with_spaces(self):
rlist = LocationService(db='test').find(
"chr1,chr1: 955,503-955,503,AGRN,chr1:955,503- 955,503,chr1: 955,503- 955,503,NIR"
)
self.assertEqual(len(rlist), 6)
def location_names_autocomplete(request, db, prefix=''):
"""Return gene names starting with *prefix*."""
ans = LocationService(db).autocomplete_name(prefix, maxi=10)
return JsonResponse(ans, safe=False)
def test_find_inexistent_feat(self):
rlist = LocationService(db='test').find("chr77")
self.assertEqual(rlist, [])
