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Utilities for VCF files.
def walk_together(*readers, **kwargs):
Simultaneously iteratate over two or more VCF readers. For each
genomic position with a variant, return a list of size equal to the number
of VCF readers. This list contains the VCF record from readers that have
this variant, and None for readers that don't have it.
The caller must make sure that inputs are sorted in the same way and use the
same reference otherwise behaviour is undefined.
vcf_record_sort_key: function that takes a VCF record and returns a
tuple that can be used as a key for comparing and sorting VCF
records across all readers. This tuple defines what it means for two
variants to be equal (eg. whether it's only their position or also
their allele values), and implicitly determines the chromosome
ordering since the tuple's 1st element is typically the chromosome
name (or calculated from it).
if 'vcf_record_sort_key' in kwargs:
get_key = kwargs['vcf_record_sort_key']
get_key = lambda r: (r.CHROM, r.POS) #, r.REF, r.ALT)
nexts = []
for reader in readers:
except StopIteration:
min_k = (None,) # keep track of the previous min key's contig
while any([r is not None for r in nexts]):
next_idx_to_k = dict(
(i, get_key(r)) for i, r in enumerate(nexts) if r is not None)
keys_with_prev_contig = [
k for k in next_idx_to_k.values() if k[0] == min_k[0]]
if any(keys_with_prev_contig):
min_k = min(keys_with_prev_contig) # finish previous contig
min_k = min(next_idx_to_k.values()) # move on to next contig
min_k_idxs = set([i for i, k in next_idx_to_k.items() if k == min_k])
yield [nexts[i] if i in min_k_idxs else None for i in range(len(nexts))]
for i in min_k_idxs:
nexts[i] = readers[i].next()
except StopIteration:
nexts[i] = None
def trim_common_suffix(*sequences):
Trim a list of sequences by removing the longest common suffix while
leaving all of them at least one character in length.
Standard convention with VCF is to place an indel at the left-most
position, but some tools add additional context to the right of the
sequences (e.g. samtools). These common suffixes are undesirable when
comparing variants, for example in variant databases.
>>> trim_common_suffix('TATATATA', 'TATATA')
['TAT', 'T']
>>> trim_common_suffix('ACCCCC', 'ACCCCCCCC', 'ACCCCCCC', 'ACCCCCCCCC')
['A', 'ACCC', 'ACC', 'ACCCC']
if not sequences:
return []
reverses = [seq[::-1] for seq in sequences]
rev_min = min(reverses)
rev_max = max(reverses)
if len(rev_min) < 2:
return sequences
for i, c in enumerate(rev_min[:-1]):
if c != rev_max[i]:
if i == 0:
return sequences
return [seq[:-i] for seq in sequences]
return [seq[:-(i + 1)] for seq in sequences]