API¶
vcf.Reader¶
-
class
vcf.
Reader
(fsock=None, filename=None, compressed=None, prepend_chr=False, strict_whitespace=False, encoding='ascii')[source]¶ Reader for a VCF v 4.0 file, an iterator returning
_Record objects
-
alts
= None¶ ALT fields from header
-
contigs
= None¶ contig fields from header
-
fetch
(chrom, start=None, end=None)[source]¶ Fetches records from a tabix-indexed VCF file and returns an iterable of
_Record
instanceschrom must be specified.
The start and end coordinates are in the zero-based, half-open coordinate system, similar to
_Record.start
and_Record.end
. The very first base of a chromosome is index 0, and the the region includes bases up to, but not including the base at the end coordinate. For examplefetch('4', 10, 20)
would include all variants overlapping a 10 base pair region from the 11th base of through the 20th base (which is at index 19) of chromosome 4. It would not include the 21st base (at index 20). See http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms for more information on the zero-based, half-open coordinate system.If end is omitted, all variants from start until the end of the chromosome chrom will be included.
If start and end are omitted, all variants on chrom will be returned.
requires pysam
-
filters
= None¶ FILTER fields from header
-
formats
= None¶ FORMAT fields from header
-
infos
= None¶ INFO fields from header
-
metadata
= None¶ metadata fields from header (string or hash, depending)
-
vcf.Writer¶
vcf.model._Record¶
-
class
vcf.model.
_Record
(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, sample_indexes, samples=None)[source]¶ A set of calls at a site. Equivalent to a row in a VCF file.
The standard VCF fields CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO and FORMAT are available as properties.
The list of genotype calls is in the
samples
property.Regarding the coordinates associated with each instance:
POS
, per VCF specification, is the one-based index (the first base of the contig has an index of 1) of the first base of theREF
sequence.- The
start
andend
denote the coordinates of the entireREF
sequence in the zero-based, half-open coordinate system (see http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms), where the first base of the contig has an index of 0, and the interval runs up to, but does not include, the base at theend
index. This indexing scheme is analagous to Python slice notation. - The
affected_start
andaffected_end
coordinates are also in the zero-based, half-open coordinate system. These coordinates indicate the precise region of the reference genome actually affected by the events denoted inALT
(i.e., the minimumaffected_start
and maximumaffected_end
).- For SNPs and structural variants, the affected region
includes all bases of
REF
, including the first base (i.e.,affected_start = start = POS - 1
). - For deletions, the region includes all bases of
REF
except the first base, which flanks upstream the actual deletion event, per VCF specification. - For insertions, the
affected_start
andaffected_end
coordinates represent a 0 bp-length region between the two flanking bases (i.e.,affected_start
=affected_end
). This is analagous to Python slice notation (see http://stackoverflow.com/a/2947881/38140). Neither the upstream nor downstream flanking bases are included in the region.
- For SNPs and structural variants, the affected region
includes all bases of
-
POS
= None¶ the one-based coordinate of the first nucleotide in
REF
-
aaf
¶ A list of allele frequencies of alternate alleles. NOTE: Denominator calc’ed from _called_ genotypes.
-
affected_end
= None¶ zero-based, half-open end coordinate of affected region of reference genome (not included in the region)
-
affected_start
= None¶ zero-based, half-open start coordinate of affected region of reference genome
-
alleles
= None¶ list of alleles. [0] = REF, [1:] = ALTS
-
call_rate
¶ The fraction of genotypes that were actually called.
-
end
= None¶ zero-based, half-open end coordinate of
REF
-
heterozygosity
¶ Heterozygosity of a site. Heterozygosity gives the probability that two randomly chosen chromosomes from the population have different alleles, giving a measure of the degree of polymorphism in a population.
If there are i alleles with frequency p_i, H=1-sum_i(p_i^2)
-
is_deletion
¶ Return whether or not the INDEL is a deletion
-
is_filtered
¶ Return True if a variant has been filtered
-
is_indel
¶ Return whether or not the variant is an INDEL
-
is_monomorphic
¶ Return True for reference calls
-
is_snp
¶ Return whether or not the variant is a SNP
-
is_sv
¶ Return whether or not the variant is a structural variant
-
is_sv_precise
¶ Return whether the SV cordinates are mapped to 1 b.p. resolution.
-
is_transition
¶ Return whether or not the SNP is a transition
-
nucl_diversity
¶ pi_hat (estimation of nucleotide diversity) for the site. This metric can be summed across multiple sites to compute regional nucleotide diversity estimates. For example, pi_hat for all variants in a given gene.
Derived from: “Population Genetics: A Concise Guide, 2nd ed., p.45” John Gillespie.
-
num_called
¶ The number of called samples
-
num_het
¶ The number of heterozygous genotypes
-
num_hom_alt
¶ The number of homozygous for alt allele genotypes
-
num_hom_ref
¶ The number of homozygous for ref allele genotypes
-
num_unknown
¶ The number of unknown genotypes
-
samples
= None¶ list of
_Calls
for each sample ordered as in source VCF
-
start
= None¶ zero-based, half-open start coordinate of
REF
-
sv_end
¶ Return the end position for the SV
-
var_subtype
¶ Return the subtype of variant.
For SNPs and INDELs, yeild one of: [ts, tv, ins, del]
For SVs yield either “complex” or the SV type defined in the ALT fields (removing the brackets). E.g.:
<DEL> -> DEL <INS:ME:L1> -> INS:ME:L1 <DUP> -> DUP
The logic is meant to follow the rules outlined in the following paragraph at:
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
“For precisely known variants, the REF and ALT fields should contain the full sequences for the alleles, following the usual VCF conventions. For imprecise variants, the REF field may contain a single base and the ALT fields should contain symbolic alleles (e.g. <ID>), described in more detail below. Imprecise variants should also be marked by the presence of an IMPRECISE flag in the INFO field.”
-
var_type
¶ Return the type of variant [snp, indel, unknown] TO DO: support SVs
vcf.model._Call¶
-
class
vcf.model.
_Call
(site, sample, data)[source]¶ A genotype call, a cell entry in a VCF file
-
data
¶ Namedtuple of data from the VCF file
-
gt_bases
¶ The actual genotype alleles. E.g. if VCF genotype is 0/1, return A/G
-
gt_type
¶ The type of genotype. hom_ref = 0 het = 1 hom_alt = 2 (we don;t track _which+ ALT) uncalled = None
-
is_filtered
¶ Return True for filtered calls
-
is_het
¶ Return True for heterozygous calls
-
is_variant
¶ Return True if not a reference call
-
phased
¶ A boolean indicating whether or not the genotype is phased for this sample
-
sample
¶ The sample name
-
site
¶ The
_Record
for this_Call
-
vcf.model._AltRecord¶
-
class
vcf.model.
_AltRecord
(type, **kwargs)[source]¶ An alternative allele record: either replacement string, SV placeholder, or breakend
-
type
= None¶ String to describe the type of variant, by default “SNV” or “MNV”, but can be extended to any of the types described in the ALT lines of the header (e.g. “DUP”, “DEL”, “INS”...)
-
vcf.model._Substitution¶
vcf.model._SingleBreakend¶
vcf.model._Breakend¶
-
class
vcf.parser.
_Breakend
(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly, **kwargs)[source]¶ A breakend which is paired to a remote location on or off the genome
-
connectingSequence
= None¶ The breakpoint’s connecting sequence.
-
orientation
= None¶ The orientation of breakend. If the sequence 3’ of the breakend is connected, True, else if the sequence 5’ of the breakend is connected, False.
-
remoteOrientation
= None¶ The orientation of breakend’s mate. If the sequence 3’ of the breakend’s mate is connected, True, else if the sequence 5’ of the breakend’s mate is connected, False.
-
withinMainAssembly
= None¶ If the breakend mate is within the assembly, True, else False if the breakend mate is on a contig in an ancillary assembly file.
-