Records 

vcfpy.Record 

class vcfpy.Record(CHROM: str, POS: int, ID: list[str], REF: str, ALT: list[AltRecord], QUAL: float | None, FILTER: list[str], INFO: dict[str, Any], FORMAT: list[str] | None = None, calls: Sequence[Call | UnparsedCall] | None = None)[source]

Represent one record from the VCF file

Record objects are iterators of their calls

ALT: list[AltRecord]: A list of alternative allele records of type AltRecord

CHROM: A str with the chromosome name

FILTER: A list of strings for the FILTER column

FORMAT: A list of strings for the FORMAT column. Optional, must be given if and only if calls is also given.

ID: A list of the semicolon-separated values of the ID column

INFO: An OrderedDict giving the values of the INFO column, flags are mapped to True

POS: An int with a 1-based begin position

QUAL: The quality value, can be None

REF: A str with the REF value

add_filter(label: str)[source]: Add label to FILTER if not set yet, removing PASS entry if present

add_format(key: str, value: Any | None = None)[source]

Add an entry to format

The record’s calls data[key] will be set to value if not yet set and value is not None. If key is already in FORMAT then nothing is done.

property affected_end

Return affected start position in 0-based coordinates

For SNVs, MNVs, and deletions, the behaviour is based on the start position and the length of the REF. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with affected_start()

property affected_start

Return affected start position in 0-based coordinates

For SNVs, MNVs, and deletions, the behaviour is the start position. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with affected_end()

begin: An int with a 0-based begin position

call_for_sample: A mapping from sample name to entry in self.calls.

calls: A list of genotype Call objects. Optional, must be given if and only if FORMAT is also given.

end: An int with a 0-based end position

is_snv()[source]: Return True if it is a SNV

update_calls(calls: Sequence[Call | UnparsedCall])[source]: Update self.calls and other fields as necessary.

vcfpy.Call 

class vcfpy.Call(sample: str, data: dict[str, Any], site: Record | None = None)[source]

The information for a genotype callable

By VCF, this should always include the genotype information and can contain an arbitrary number of further annotation, e.g., the coverage at the variant position.

called: whether or not the variant is fully called

data: dict[str, Any]: an OrderedDict with the key/value pair information from the call’s data

gt_alleles: list[int | None] | None: the allele numbers (0, 1, …) in this calls or None for no-call

property gt_bases: tuple[str | None, ...]: Return the actual genotype bases, e.g. if VCF genotype is 0/1, could return (‘A’, ‘T’)

property gt_phase_char: Return character to use for phasing

property gt_type: Literal[0, 1, 2] | None: The type of genotype, returns one of HOM_REF, HOM_ALT, and HET.

is_filtered(require: list[str] | None = None, ignore: list[str] | None = None)[source]

Return True for filtered calls

Parameters:

ignore (iterable) – if set, the filters to ignore, make sure to include ‘PASS’, when setting, default is ['PASS']
require (iterable) – if set, the filters to require for returning True

property is_het: bool: Return True for heterozygous calls

property is_phased: Return boolean indicating whether this call is phased

property is_variant: bool: Return True for non-hom-ref calls

ploidy: the number of alleles in this sample’s call

sample: the name of the sample for which the call was made

set_genotype(genotype: str | None)[source]: Set self.data["GT"] to genotype and properly update related properties.

site: the Record of this Call

vcfpy.AltRecord 

class vcfpy.AltRecord(type_: Literal['SNV', 'MNV', 'DEL', 'INS', 'INDEL', 'SV', 'BND', 'SYMBOLIC', 'MIXED'] | None = None)[source]

An alternative allele Record

Currently, can be a substitution, an SV placeholder, or breakend

serialize() → str[source]: Return str with representation for VCF file

type: String describing the type of the variant, could be one of SNV, MNV, could be any of teh types described in the ALT header lines, such as DUP, DEL, INS, …

vcfpy.Substitution 

class vcfpy.Substitution(type_: Literal['SNV', 'MNV', 'DEL', 'INS', 'INDEL', 'SV', 'BND', 'SYMBOLIC', 'MIXED'], value: str)[source]

A basic alternative allele record describing a REF->AltRecord substitution

Note that this subsumes MNVs, insertions, and deletions.

serialize() → str[source]: Return str with representation for VCF file

value: The alternative base sequence to use in the substitution

vcfpy.SV 

vcfpy.SV: alias of SV

vcfpy.BreakEnd 

A placeholder for a breakend

mate_chrom: chromosome of the mate breakend

mate_orientation: orientation breakend’s mate

mate_pos: position of the mate breakend

orientation: orientation of this breakend

sequence: breakpoint’s connecting sequence

serialize()[source]: Return string representation for VCF

within_main_assembly: bool specifying if the breakend mate is within the assembly (True) or in an ancillary assembly (False)

vcfpy.SingleBreakEnd 

class vcfpy.SingleBreakEnd(orientation: str, sequence: str)[source]: A placeholder for a single breakend

vcfpy.SymbolicAllele 

class vcfpy.SymbolicAllele(value: str)[source]

A placeholder for a symbolic allele

The allele symbol must be defined in the header using an ALT header before being parsed. Usually, this is used for succinct descriptions of structural variants or IUPAC parameters.

serialize()[source]: Return str with representation for VCF file

value: The symbolic value, e.g. ‘DUP’