API¶
vcf.Reader¶
-
class
vcf.
Reader
(fsock=None, filename=None, compressed=False, prepend_chr=False)[source]¶ Reader for a VCF v 4.0 file, an iterator returning
_Record objects
-
alts
= None¶ ALT fields from header
-
fetch
(chrom, start, end=None)[source]¶ fetch records from a Tabix indexed VCF, requires pysam if start and end are specified, return iterator over positions if end not specified, return individual
_Call
at start or None
-
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.-
aaf
¶ The allele frequency of the alternate allele. NOTE 1: Punt if more than one alternate allele. NOTE 2: Denominator calc’ed from _called_ genotypes.
-
alleles
= None¶ list of alleles. [0] = REF, [1:] = ALTS
-
call_rate
¶ The fraction of genotypes that were actually called.
-
end
= None¶ 1-based end coordinate
-
is_deletion
¶ Return whether or not the INDEL is a deletion
-
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¶ 0-based start coordinate
-
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> -> DUPThe 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
-
called
¶ True if the GT is not ./.
-
data
¶ Dictionary of data from the VCF file
-
gt_alleles
¶ The numbers of the alleles called at a given sample
-
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_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
-
chr
= None¶ The chromosome of breakend’s mate.
-
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.
-
pos
= None¶ The coordinate of breakend’s mate.
-
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.
-