def make_snp_genome_variant_on_end_tag_unable_to_span(vv=1, gv_id=12):
seq = "CGCACCGGAACTTGTGTTTGTGTGTGTGATCGCCCACTACGCACGTTATATG".lower()
tv = make_tile_variant(int('3'+vv_min,16)+vv, seq, 1, end_tag="ATCGCCCACTACGCACGTTATATG")
gv = make_genome_variant(gv_id, 106, 107, 'G', 'A')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=28, end=29)
gvt.save()
return tv, gv, gvt
def make_basic_del_genome_variant(vv=3, gv_id=3):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 26, "CG", "-")
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=24, end=24)
gvt.save()
return tv, gv, gvt
def make_spanning_4_del_genome_variant(vv=10, gv_id=10):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCGTCAGAATGTTTGGAGGGCGGTACGCACCGGAACTTGTGTTTGTGTGTGTGGTCGCCCACTACGCACGTTATATG".lower()
tv = make_tile_variant(vv, seq, 4, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT", end_tag="GTCGCCCACTACGCACGTTATATG")
gv = make_genome_variant(gv_id, 49, 79, 'GGCTAGAGATATCACCCTCTGCTACTCAAC', '-')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=49, end=49)
gvt.save()
return tv, gv, gvt
def make_snp_genome_variant_on_start_tag_unable_to_span(vv=11, gv_id=11):
seq = "ACGGCAGTAGTTTTGCCGCTCGGCGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGC")
gv = make_genome_variant(gv_id, 23, 24, 'T', '-')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=23, end=23)
gvt.save()
return tv, gv, gvt
def make_spanning_2_ins_genome_variant(vv=8, gv_id=8):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCGTTTTCAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower()
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 26, 26, '-', 'TTT')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=26, end=29)
gvt.save()
return tv, gv, gvt
def make_spanning_2_sub_genome_variant(vv=6, gv_id=6):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCACAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower()
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 25, 27, 'GT', 'A')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=25, end=26)
gvt.save()
return tv, gv, gvt
def make_basic_ins_genome_variant(vv=4, gv_id=4):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTAAACGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 24, '-', 'AAA')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=24, end=27)
gvt.save()
return tv, gv, gvt
def make_basic_snp_genome_variant(vv=1, gv_id=1):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 25, 'C', 'T')
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=24, end=25)
gvt.save()
return tv, gv, gvt
def make_basic_snp_genome_variant(vv=1, gv_id=1):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 25, 'C', 'T')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=25)
gvt.save()
return tv, gv, gvt
def make_basic_del_genome_variant(vv=3, gv_id=3):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 26, "CG", "-")
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=24)
gvt.save()
return tv, gv, gvt
def make_snp_genome_variant_on_start_tag_unable_to_span(vv=11, gv_id=11):
seq = "ACGGCAGTAGTTTTGCCGCTCGGCGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGC")
gv = make_genome_variant(gv_id, 23, 24, 'T', '-')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=23,
end=23)
gvt.save()
return tv, gv, gvt
def make_basic_ins_genome_variant(vv=4, gv_id=4):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTAAACGTCAGAATGTTTGGAGGGCGGTACG".lower()
tv = make_tile_variant(vv, seq, 1, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 24, '-', 'AAA')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=27)
gvt.save()
return tv, gv, gvt
def make_spanning_3_del_genome_variant(vv=9, gv_id=9):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCGTCAGAATGTTTGGAGGGCGGTACAGAGATATCACCCTCTGCTACTCAACGCACCGGAACTTGTGTTTGTGTG".lower(
)
tv = make_tile_variant(vv, seq, 3, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 49, 53, 'GGCT', '-')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=49,
end=49)
gvt.save()
return tv, gv, gvt
def make_spanning_2_ins_genome_variant(vv=8, gv_id=8):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCGTTTTCAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 26, 26, '-', 'TTT')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=26,
end=29)
gvt.save()
return tv, gv, gvt
def make_spanning_2_sub_genome_variant(vv=6, gv_id=6):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTCACAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 25, 27, 'GT', 'A')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=25,
end=26)
gvt.save()
return tv, gv, gvt
def make_broken_genome_variant():
v = '0'*NUM_HEX_INDEXES_FOR_VERSION
p = '0'*(NUM_HEX_INDEXES_FOR_PATH)
s = '0'*(NUM_HEX_INDEXES_FOR_STEP-1)+'3'
vv = hex(1).lstrip('0x').zfill(NUM_HEX_INDEXES_FOR_VARIANT_VALUE)
seq = "CGCACCGGAACTTGTGTTTGTGTGTGTGGTCGCCCACTACGCACGTTATATGAGAGCTGGCAGATGCCTTATGGAAGTGACTGCTACCGTTTGTTGACAC".lower()
tv = make_tile_variant(int(v+p+s+vv,16), seq, 2)
gv = make_genome_variant(0, 129, 131, "GA", "-")
gvt = GenomeVariantTranslation(tile_variant=tv, genome_variant=gv, start=53, end=53)
gvt.save()
return tv, gv, gvt
def make_snp_genome_variant_on_end_tag_unable_to_span(vv=1, gv_id=12):
seq = "CGCACCGGAACTTGTGTTTGTGTGTGTGATCGCCCACTACGCACGTTATATG".lower()
tv = make_tile_variant(int('3' + vv_min, 16) + vv,
seq,
1,
end_tag="ATCGCCCACTACGCACGTTATATG")
gv = make_genome_variant(gv_id, 106, 107, 'G', 'A')
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=28,
end=29)
gvt.save()
return tv, gv, gvt
def make_two_genome_variants_for_one_tile_variant(vv=1, gv_id=1):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTACAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 25, "C", "T")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=25).save()
gv2 = make_genome_variant(gv_id + 1, 25, 27, "GT", "A")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv2,
start=25,
end=26).save()
def make_two_genome_variants_for_one_tile_variant_alter_translation_indexes(
vv=1, gv_id=1):
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTTTTCAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(vv, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
gv = make_genome_variant(gv_id, 24, 26, "CG", "-")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=24).save()
gv = make_genome_variant(gv_id + 1, 26, 26, "-", "TTT")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=27).save()
def make_broken_genome_variant():
v = '0' * NUM_HEX_INDEXES_FOR_VERSION
p = '0' * (NUM_HEX_INDEXES_FOR_PATH)
s = '0' * (NUM_HEX_INDEXES_FOR_STEP - 1) + '3'
vv = hex(1).lstrip('0x').zfill(NUM_HEX_INDEXES_FOR_VARIANT_VALUE)
seq = "CGCACCGGAACTTGTGTTTGTGTGTGTGGTCGCCCACTACGCACGTTATATGAGAGCTGGCAGATGCCTTATGGAAGTGACTGCTACCGTTTGTTGACAC".lower(
)
tv = make_tile_variant(int(v + p + s + vv, 16), seq, 2)
gv = make_genome_variant(0, 129, 131, "GA", "-")
gvt = GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=53,
end=53)
gvt.save()
return tv, gv, gvt
def make_entire_library(multiple_assemblies=False):
make_reference(multiple_assemblies=multiple_assemblies)
tv, basic_snp, trans = make_basic_snp_genome_variant()
make_basic_sub_genome_variant()
tv, basic_del, trans = make_basic_del_genome_variant()
make_basic_ins_genome_variant()
make_spanning_2_snp_genome_variant()
tv, spanning_sub, trans = make_spanning_2_sub_genome_variant()
make_spanning_2_del_genome_variant()
tv, spanning_ins, trans = make_spanning_2_ins_genome_variant()
make_spanning_3_del_genome_variant()
make_spanning_4_del_genome_variant()
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTACAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(11, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=basic_snp,
start=24,
end=25).save()
GenomeVariantTranslation(tile_variant=tv,
genome_variant=spanning_sub,
start=25,
end=26).save()
seq = "ACGGCAGTAGTTTTGCCGCTCGGTTTTTCAGAATGTTTGGAGGGCGGTACGGCTAGAGATATCACCCTCTGCTACTC".lower(
)
tv = make_tile_variant(12, seq, 2, start_tag="ACGGCAGTAGTTTTGCCGCTCGGT")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=basic_del,
start=24,
end=24).save()
GenomeVariantTranslation(tile_variant=tv,
genome_variant=spanning_ins,
start=24,
end=27).save()
make_snp_genome_variant_on_start_tag_unable_to_span(vv=13, gv_id=11)
seq = "TAGAGATATCACCCTCTGCTACTCCGCACCGGAACTTGTGTTTGTGTG".lower()
tv = make_tile_variant(int('2' + vv_min, 16) + 1, seq, 1)
gv = make_genome_variant(12, 76, 78, "AA", "-")
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=24,
end=24).save()
if multiple_assemblies:
tv = TileVariant.objects.get(tile_variant_int=int('2' + vv_min, 16) +
2)
else:
seq = "TAGAGATATCACCCTCTGCTACTCAACGCACCGGAACTTGTGTTTGTGTTTGTGGTCGCCCACTACGCACGTTATATG".lower(
)
tv = make_tile_variant(int('2' + vv_min, 16) + 2,
seq,
2,
end_tag="GTCGCCCACTACGCACGTTATATG")
gv = make_genome_variant(13, 101, 102, 'G', 'T')
GenomeVariantTranslation(tile_variant=tv,
genome_variant=gv,
start=49,
end=50).save()
make_snp_genome_variant_on_end_tag_unable_to_span(vv=1, gv_id=14)