def test_basic(self):
seq_str = 'ATGCATGCATGCACTG'
filters = 'hola'
alleles1 = {('A', SNP):{'read_groups': {'hola_illumina':2, 'hola2':3}},
('T', INVARIANT):{'read_groups': {'sanger':5, 'hola2':4}},
('C', SNP):{'read_groups': {'hola_illumina':6}}}
read_groups = {'hola_illumina':{'LB':'lib1'},
'hola2':{'LB':'lib2'},
'sanger': {'LB': 'lib3'}}
snv1 = SeqFeature(type='snv', location=FeatureLocation(4, 4),
qualifiers={'alleles':alleles1, 'reference_allele':'T',
'filters':filters, 'read_groups':read_groups})
alleles2 = {('T', INVARIANT):{'read_groups': {'hola_illumina':1}},
('---', DELETION):{'read_groups': {'hola_illumina':1}}}
snv2 = SeqFeature(type='snv', location=FeatureLocation(8, 8),
qualifiers={'alleles':alleles2, 'reference_allele':'T',
'read_groups':read_groups})
alleles3 = {('AT', INSERTION):{'read_groups': {'hola_illumina':1}},
('T', INVARIANT):{'read_groups': {'hola_illumina':1}}}
snv3 = SeqFeature(type='snv', location=FeatureLocation(12, 12),
qualifiers={'alleles':alleles3, 'reference_allele':'T'})
seq = SeqWithQuality(seq=Seq(seq_str), qual=[30] * len(seq_str),
name='AT1G55265.1', features=[snv1, snv2, snv3])
# try with SNP
fhand = NamedTemporaryFile(mode='a')
writer = SnvSequenomWriter(fhand)
position = 4
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
assert 'ATGC[T/A/C]TGCNNNCANNCTG' in sequenom_snv
# try with Deletion
fhand = NamedTemporaryFile(mode='a')
writer = SnvSequenomWriter(fhand)
position = 8
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
assert 'ATGCHTGC[ATG/-]CANNCTG' in sequenom_snv
# try with Insertion
fhand = NamedTemporaryFile(mode='a')
writer = SnvSequenomWriter(fhand)
position = 12
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
assert 'ATGCHTGCNNNC[-/AT]CTG' in sequenom_snv
def test_basic(self):
seq_str = "ATGCATGCATGCACTG"
# 'ATGCATGCATGCA-CTG'
# 'ATGCNTGCA---ATCTG'
filters = "hola"
alleles1 = {
("T", SNP): {"read_groups": {"hola_illumina": 2, "hola2": 3}},
("A", INVARIANT): {"read_groups": {"sanger": 5, "hola2": 4}},
("C", SNP): {"read_groups": {"hola_illumina": 6}},
}
read_groups = {"hola_illumina": {"LB": "lib1"}, "hola2": {"LB": "lib2"}, "sanger": {"LB": "lib3"}}
snv1 = SeqFeature(
type="snv",
location=FeatureLocation(4, 5),
qualifiers={"alleles": alleles1, "reference_allele": "A", "filters": filters, "read_groups": read_groups},
)
alleles2 = {
("ATGC", INVARIANT): {"read_groups": {"hola_illumina": 1}},
("A", DELETION): {"read_groups": {"hola_illumina": 1}},
}
snv2 = SeqFeature(
type="snv",
location=FeatureLocation(8, 12),
qualifiers={"alleles": alleles2, "reference_allele": "ATGC", "read_groups": read_groups},
)
alleles3 = {
("AT", INSERTION): {"read_groups": {"hola_illumina": 1}},
("A", INVARIANT): {"read_groups": {"hola_illumina": 1}},
}
snv3 = SeqFeature(
type="snv", location=FeatureLocation(12, 13), qualifiers={"alleles": alleles3, "reference_allele": "A"}
)
seq = SeqWithQuality(
seq=Seq(seq_str), qual=[30] * len(seq_str), name="AT1G55265.1", features=[snv1, snv2, snv3]
)
# try with SNP
fhand = NamedTemporaryFile(mode="a")
writer = SnvSequenomWriter(fhand)
position = 4
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
# print sequenom_snv
assert "ATGC[C/A/T]TGCANNNNCTG" in sequenom_snv
# untill we solve the sequenom format for not SNP we can not do this test
return
# try with Deletion
fhand = NamedTemporaryFile(mode="a")
writer = SnvSequenomWriter(fhand)
position = 8
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
# print sequenom_snv
assert "ATGCHTGC[ATGC/A]NCTG" in sequenom_snv
# try with Insertion
fhand = NamedTemporaryFile(mode="a")
writer = SnvSequenomWriter(fhand)
position = 12
writer.write(seq, position)
sequenom_snv = open(fhand.name).read()
assert "ATGCHTGCNNNC[A/AT]CTG" in sequenom_snv