def reverse_indel(var, genome):
''' reverse an indel (with only one alt allele)
'''
ref = revcomp(var.ref)
alt = revcomp(var.alts[0])
var.pos -= len(ref)
_, chrom = prefix_chrom(var)
if len(ref) > len(alt): # handle deletions
ref = ref[:-len(alt)]
alt = genome[chrom][var.pos].seq
ref = alt + ref
elif len(alt) > len(ref): # handle insertions
alt = alt[:-len(ref)]
ref = genome[chrom][var.pos].seq
alt = ref + alt
var.ref, var.alts = ref, [alt]
# TODO: reject indels spanning multiple mapping regions. We could remap the
# TODO: start position, then add the length to get a predicted end position.
# TODO: Then check if this is different from an end position determined by
# TODO: getting an original end position, then remapping.
return var
def remap(converter, var, genome):
''' converts variant coordinates between genome versions
Args:
converter: pyLiftover.LiftOver object, for the from and to genome builds
var: variant to be converted
genome: pyfaidx.Fasta object for reference genome being converted to
'''
prefixed, chrom = prefix_chrom(var)
try:
chrom, pos, strand = get_new_coords(converter, chrom, var.pos)
except ValueError:
return None
if not prefixed:
chrom = chrom.strip('chr')
if chrom not in CHROMS:
return None
# set updated coords, and convert back from 0-indexed position
var.chrom = chrom
var.pos = pos
if strand == '-':
var = reverse_var(var, genome)
if var is not None:
var.pos += 1
return var
def test_prefix_chrom_existing(self):
var = self.Var()
var.chrom = 'chr1'
prefixed, chrom = prefix_chrom(var)
self.assertTrue(prefixed)
self.assertEqual(chrom, 'chr1')
def test_prefix_chrom(self):
var = self.Var()
var.chrom = '1'
prefixed, chrom = prefix_chrom(var)
self.assertFalse(prefixed)
self.assertEqual(chrom, 'chr1')
def reverse_cnv(var, genome):
''' reverse a CNV
'''
_, chrom = prefix_chrom(var)
var.pos -= int(var.info['SVLEN'])
var.ref = genome[chrom][var.pos].seq
# TODO: reject CNVs spanning multiple mapping regions
return var
def check_reference(var, genome):
''' account for variants where the reference sequence has changed.
This also requires GT, PL and AD fields, and various info fields to be
adjusted, if present.
'''
_, chrom = prefix_chrom(var)
end = var.pos + len(var.ref)
ref_base = genome[chrom][var.pos:end].seq
if ref_base == var.ref:
return var
if ref_base not in var.alts:
return None
idx = var.alts.index(ref_base)
var.alts[idx] = var.ref
var.ref = ref_base
return var