def test_vanilla(self):
dummy = Genome(name='GRCh37.75_Y-Only', SNPs='dummySRY_AGN')
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('HTGCAATCATATGCTTCTGC', persProt.transcript.cDNA[:20])
def test_noModif(self) : from pyGeno.SNPFiltering import SNPFilter class MyFilter(SNPFilter) : def __init__(self) : SNPFilter.__init__(self) def filter(self, chromosome, dummySRY_AGN) : return None dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN', SNPFilter = MyFilter()) persProt = dummy.get(Protein, id = 'ENSP00000438917')[0] refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0] self.assertEqual(persProt.transcript.cDNA[:20], refProt.transcript.cDNA[:20])
def test_SNP(self) :
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter) :
def __init__(self) :
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN) :
from pyGeno.SNPFiltering import SequenceSNP
return SequenceSNP(dummySRY_AGN.alt)
dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN', SNPFilter = MyFilter())
persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
self.assertEqual('M', refProt.sequence[0])
self.assertEqual('L', persProt.sequence[0])
def test_deletion(self) :
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter) :
def __init__(self) :
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN) :
from pyGeno.SNPFiltering import SequenceDel
refAllele = chromosome.refSequence[dummySRY_AGN.start]
return SequenceDel(1)
dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY_AGN', SNPFilter = MyFilter())
persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('TGCAATCATATGCTTCTGCT', persProt.transcript.cDNA[:20])
def test_indels(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN_indels):
from pyGeno.SNPFiltering import SequenceInsert
ret = ""
for s in dummySRY_AGN_indels:
ret += "X"
return SequenceInsert(ret)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN_indels',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('XXXATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
class pyGenoSNPTests(unittest.TestCase):
def setUp(self):
# try :
# B.importGenome("Human.GRCh37.75_Y-Only.tar.gz")
# except KeyError :
# deleteGenome("human", "GRCh37.75_Y-Only")
# B.importGenome("Human.GRCh37.75_Y-Only.tar.gz")
# print "--> Seems to already exist in db"
# try :
# B.importSNPs("Human_agnostic.dummySRY.tar.gz")
# except KeyError :
# deleteSNPs("dummySRY_AGN")
# B.importSNPs("Human_agnostic.dummySRY.tar.gz")
# print "--> Seems to already exist in db"
# try :
# B.importSNPs("Human_agnostic.dummySRY_indels")
# except KeyError :
# deleteSNPs("dummySRY_AGN_indels")
# B.importSNPs("Human_agnostic.dummySRY_indels")
# print "--> Seems to already exist in db"
self.ref = Genome(name='GRCh37.75_Y-Only')
def tearDown(self):
pass
# @unittest.skip("skipping")
def test_vanilla(self):
dummy = Genome(name='GRCh37.75_Y-Only', SNPs='dummySRY_AGN')
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('HTGCAATCATATGCTTCTGC', persProt.transcript.cDNA[:20])
# @unittest.skip("skipping")
def test_noModif(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
return None
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual(persProt.transcript.cDNA[:20],
refProt.transcript.cDNA[:20])
# @unittest.skip("skipping")
def test_insert(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceInsert
refAllele = chromosome.refSequence[dummySRY_AGN.start]
return SequenceInsert('XXX')
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('XXXATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
# @unittest.skip("skipping")
def test_SNP(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceSNP
return SequenceSNP(dummySRY_AGN.alt)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('M', refProt.sequence[0])
self.assertEqual('L', persProt.sequence[0])
# @unittest.skip("skipping")
def test_deletion(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceDel
refAllele = chromosome.refSequence[dummySRY_AGN.start]
return SequenceDel(1)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('TGCAATCATATGCTTCTGCT', persProt.transcript.cDNA[:20])
# @unittest.skip("skipping")
def test_indels(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN_indels):
from pyGeno.SNPFiltering import SequenceInsert
ret = ""
for s in dummySRY_AGN_indels:
ret += "X"
return SequenceInsert(ret)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN_indels',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('XXXATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
# @unittest.skip("skipping")
def test_bags(self):
dummy = Genome(name='GRCh37.75_Y-Only')
self.assertEqual(dummy.wrapped_object, self.ref.wrapped_object)
# @unittest.skip("skipping")
def test_prot_find(self):
prot = self.ref.get(Protein, id='ENSP00000438917')[0]
needle = prot.sequence[:10]
self.assertEqual(0, prot.find(needle))
needle = prot.sequence[-10:]
self.assertEqual(len(prot) - 10, prot.find(needle))
# @unittest.skip("skipping")
def test_trans_find(self):
trans = self.ref.get(Transcript, name="SRY-001")[0]
self.assertEqual(0, trans.find(trans[:5]))
class pyGenoSNPTests(unittest.TestCase):
def setUp(self):
self.ref = Genome(name='GRCh37.75_Y-Only')
def tearDown(self):
pass
def test_vanilla(self):
dummy = Genome(name='GRCh37.75_Y-Only', SNPs='dummySRY_AGN')
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('HTGCAATCATATGCTTCTGC', persProt.transcript.cDNA[:20])
def test_noModif(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
return None
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual(persProt.transcript.cDNA[:20],
refProt.transcript.cDNA[:20])
def test_insert(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceInsert
refAllele = chromosome.refSequence[dummySRY_AGN.start]
return SequenceInsert('TCA')
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('ATGATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
def test_SNP(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceSNP
return SequenceSNP(dummySRY_AGN.alt)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('M', refProt.sequence[0])
self.assertEqual('L', persProt.sequence[0])
def test_deletion(self):
from pyGeno.SNPFiltering import SNPFilter
class MyFilter(SNPFilter):
def __init__(self):
SNPFilter.__init__(self)
def filter(self, chromosome, dummySRY_AGN):
from pyGeno.SNPFiltering import SequenceDel
refAllele = chromosome.refSequence[dummySRY_AGN.start]
return SequenceDel(1)
dummy = Genome(name='GRCh37.75_Y-Only',
SNPs='dummySRY_AGN',
SNPFilter=MyFilter())
persProt = dummy.get(Protein, id='ENSP00000438917')[0]
refProt = self.ref.get(Protein, id='ENSP00000438917')[0]
self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
self.assertEqual('TGCAATCATATGCTTCTGCT', persProt.transcript.cDNA[:20])
def test_bags(self):
dummy = Genome(name='GRCh37.75_Y-Only')
self.assertEqual(dummy.wrapped_object, self.ref.wrapped_object)
def test_prot_find(self):
prot = self.ref.get(Protein, id='ENSP00000438917')[0]
needle = prot.sequence[:10]
self.assertEqual(0, prot.find(needle))
needle = prot.sequence[-10:]
self.assertEqual(len(prot) - 10, prot.find(needle))
def test_trans_find(self):
trans = self.ref.get(Transcript, name="SRY-001")[0]
self.assertEqual(0, trans.find(trans[:5]))
def test_import_remote_genome(self):
self.assertRaises(KeyError, B.importRemoteGenome,
"Human.GRCh37.75_Y-Only.tar.gz")
def test_import_remote_snps(self):
self.assertRaises(KeyError, B.importRemoteSNPs,
"Human_agnostic.dummySRY.tar.gz")
from pyGeno.Genome import *
g = Genome(name = "GRCh37.75")
prot = g.get(Protein, id = 'ENSP00000438917')[0]
#print the protein sequence
print prot.sequence
#print the protein's gene biotype
print prot.gene.biotype
#print protein's transcript sequence
print prot.transcript.sequence
#fancy queries
for exon in g.get(Exon, {"CDS_start >": x1, "CDS_end <=" : x2, "chromosome.number" : "22"}) :
#print the exon's coding sequence
print exon.CDS
#print the exon's transcript sequence
print exon.transcript.sequence
#You can do the same for your subject specific genomes
#by combining a reference genome with polymorphisms
g = Genome(name = "GRCh37.75", SNPs = ["STY21_RNA"], SNPFilter = MyFilter())