def test_insert_long():
ref = "CCCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCT"
alt = ("CCCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCT"
"CCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCT")
vd = vcf2cshl(1, ref, alt, trimmer=trim_str_back)
assert vd.position == 2 # FIXME
def test_vcf2cshl_variant_format(ref, alt, vt, pos, length):
vd = vcf2cshl(1, ref, alt, trimmer=trim_str_back)
assert vd.position == pos
assert str(vd) == vt
assert vd.length == length
def test_spark_v3_problems_check():
# chrom = '1'
position = 865461
ref = "AGCCCCACCTTCCTCTCCTCCT"
alt = "AGCCCCACCTTCCTCTCCTCCT" "GCCCCACCTTCCTCTCCTCCT"
vd = vcf2cshl(position, ref, alt, trimmer=trim_str_back)
assert str(vd) == "ins(GCCCCACCTTCCTCTCCTCCT)"
assert vd.position == position + 1
def test_tandem_repeat_unit(chrom, position, ref, alt, unit, ref_repeats,
alt_repeats):
tr_unit, tr_ref, tr_alt = tandem_repeat(ref, alt)
assert tr_unit is not None
assert tr_ref is not None
assert tr_alt is not None
assert tr_unit == unit
assert tr_ref == ref_repeats
assert tr_alt == alt_repeats
vd = vcf2cshl(position, ref, alt)
assert vd.variant_type & VariantType.tandem_repeat
if ref_repeats < alt_repeats:
assert vd.variant_type & VariantType.insertion
elif ref_repeats > alt_repeats:
assert vd.variant_type & VariantType.deletion
def test_cshl_to_vcf_problem(genome_2013):
chrom = "2"
position = 242815433
variant = "sub(G->A)"
position1, reference, alternative = dae2vcf_variant(
chrom, position, variant, genome_2013)
print(chrom, position, reference, alternative)
assert chrom == "2"
assert position == position1
assert reference == "G"
assert alternative == "A"
vd = vcf2cshl(position, reference, alternative, trimmer=trim_str_back)
assert vd.position == position
assert str(vd) == variant
assert vd.length == 1
def from_vcf(chrom, position, reference, alternative):
return VariantDetails(chrom, vcf2cshl(position, reference,
alternative))