def test_peptides_from_varaints(self):
coding = {}
coding['NM_080751'] = MutationSyntax('NM_080751',2629,876,'c.2630C>T','p.Pro877Leu')
var = Variant('line0',0,20,2621905,'C','T',coding,True,False)
var.gene = 'TMC2'
ma = MartsAdapter(biomart="http://ensembl.org")
vars = [var, Variant("testInsertion", 2, 20, 2621899, "", "AAAAAA", {'NM_080751':MutationSyntax('NM_080751',2625,876,'c.2630C>T','p.Pro877Leu')}, True, False)]
test = Generator.generate_peptides_from_variants(vars, 9, ma, id_type=EIdentifierTypes.REFSEQ, peptides=None)
test2 = [x for x in test]
print(len(test2))
ts = list()
#using a tweaked generator that takes another sequence source if the sequence is too short in respect to the given variants
#in this case a newer/older sequence from mart in respect to what was given as reference in the annotation process
t = Generator.generate_transcripts_from_variants(vars, ma, id_type=EIdentifierTypes.REFSEQ)
ts = [x for x in t]
print(len(ts[0]))
p = Generator.generate_proteins_from_transcripts(ts, to_stop=True)
ps = [x for x in p]
e = Generator.generate_peptides_from_proteins(ps, 9)
es = [x for x in e]
print(len(es))
#print vars
print len(vars)
def test_real_life_test(self):
mart = MartsAdapter(biomart="http://grch37.ensembl.org/biomart/martservice?query=")
ano_path = os.path.join(os.path.dirname(inspect.getfile(Fred2)), "Data/examples/test_annovar.out")
vars = read_annovar_exonic(ano_path)
peps = set(map(lambda x: str(x), Generator.generate_peptides_from_variants(vars, 9, mart,
EIdentifierTypes.REFSEQ)))
peps_from_prot = set(map(str, Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(vars, mart, EIdentifierTypes.REFSEQ)), 9)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
def test_real_life_test(self):
mart = MartsAdapter(
biomart="http://grch37.ensembl.org/biomart/martservice?query=")
ano_path = os.path.join(os.path.dirname(inspect.getfile(Fred2)),
"Data/examples/test_annovar.out")
vars = read_annovar_exonic(ano_path)
peps = set(
map(
lambda x: str(x),
Generator.generate_peptides_from_variants(
vars, 9, mart, EIdentifierTypes.REFSEQ)))
peps_from_prot = set(
map(
str,
Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(
vars, mart, EIdentifierTypes.REFSEQ)), 9)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
def test_peptides_from_variants(self):
"""
Create multiple peptides, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTGGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
Resulting peptides of length 3:
KFG +
KNL +
NLG +
KFP +
FPP +
PPG +
KNF +
NFP +
FPR +
PRG +
GFK +
GGL +
GLK +
GFP +
FPP +
PPK +
GGF +
GFP +
FPQ +
PQK +
"""
dummy_db = DummyAdapter()
exp_peps = set([
'PRG', 'GLK', 'PPG', 'KFP', 'GFK', 'PPK', 'GFP', 'PQK', 'KNL',
'KFG', 'GGF', 'FPQ', 'FPP', 'NLG', 'FPR', 'KNF', 'GGL', 'NFP'
])
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
peps = set(
map(
lambda x: str(x),
Generator.generate_peptides_from_variants(
dummy_vars, 3, dummy_db, EIdentifierTypes.REFSEQ)))
peps_from_prot = set(
map(
str,
Generator.generate_peptides_from_proteins(
Generator.generate_proteins_from_transcripts(
Generator.generate_transcripts_from_variants(
dummy_vars, dummy_db, EIdentifierTypes.REFSEQ)),
3)))
self.assertTrue(len(peps - peps_from_prot) == 0)
self.assertTrue(len(peps_from_prot - peps) == 0)
self.assertTrue(len(peps - exp_peps) == 0)
self.assertTrue(len(exp_peps - peps) == 0)
def test_peptides_from_variants(self):
"""
Create multiple peptides, given a set
containing heterozygous variants .
Variants:
3-DEL(-2) , 5-INS(+3) , 7-DEL(-4)
HET-DEL(-2), HOM-INS(+3), HET-DEL(-1)
Reference sequence:
AAAAACCCCCGGGGG
AAATTTGGGGG (DEL,INS,DEL)
AAATTTCCCCCGGGGG (DEL,INS)
AAAAATTTGGGGG (INS,DEL)
AAAAATTTCCCCCGGGGG (INS)
GGGGGCCCCCAAAAA
GGGTTTCAAAAA (DEL,INS,DEL)
GGGTTTCCCCCAAAAA (DEL,INS)
GGGGGTTTCAAAAA (INS,DEL)
GGGGGTTTCCCCCAAAAA (INS)
Resulting protein sequences:
KFG
KNLG
KFPPG
KNFPRG
GFK
GGLK
GFPPK
GGFPQK
Resulting peptides of length 3:
KFG +
KNL +
NLG +
KFP +
FPP +
PPG +
KNF +
NFP +
FPR +
PRG +
GFK +
GGL +
GLK +
GFP +
FPP +
PPK +
GGF +
GFP +
FPQ +
PQK +
"""
dummy_db = DummyAdapter()
exp_peps = set(['PRG', 'GLK', 'PPG', 'KFP', 'GFK', 'PPK', 'GFP', 'PQK', 'KNL', 'KFG', 'GGF', 'FPQ',
'FPP', 'NLG', 'FPR', 'KNF', 'GGL', 'NFP'])
# 1) INS, SNP, DEL
dummy_vars = [var_10, var_11, var_12]
peps = set(map(lambda x: str(x), Generator.generate_peptides_from_variants(dummy_vars, 3, dummy_db)))
self.assertTrue(len(peps-exp_peps) == 0)
self.assertTrue(len(exp_peps-peps) == 0)
