Records ¶

Contents

Records

vcfpy.Record ¶

class vcfpy.Record(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, calls)[source]¶

Represent one record from the VCF file

Record objects are iterators of their calls

ALT = None¶: A list of alternative allele records of type AltRecord

CHROM = None¶: A str with the chromosome name

FILTER = None¶: A list of strings for the FILTER column

FORMAT = None¶: A list of strings for the FORMAT column

ID = None¶: A list of the semicolon-separated values of the ID column

INFO = None¶: An OrderedDict giving the values of the INFO column, flags are mapped to True

POS = None¶: An int with a 1-based begin position

QUAL = None¶: The quality value, can be None

REF = None¶: A str with the REF value

add_filter(label)[source]¶: Add label to FILTER if not set yet

add_format(key, value=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.

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 :py:method:`affected_start`

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 :py:method:`affected_end`

begin = None¶: An int with a 0-based begin position

call_for_sample = None¶: A mapping from sample name to entry in self.calls

calls = None¶: A list of genotype Call objects

end = None¶: An int with a 0-based end position

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

vcfpy.Call ¶

class vcfpy.Call(sample, data, site=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 = None¶: whether or not the variant is fully called

data = None¶: an OrderedDict with the key/value pair information from the call’s data

gt_alleles = None¶: the allele numbers (0, 1, ...) in this calls or None for no-call

gt_bases¶: Return the actual genotype alleles, e.g. if VCF genotype is 0/1, could return A/T

gt_phase_char()[source]¶: Return character to use for phasing

gt_type¶

The type of genotype, mapping is

hom_ref = 0
het = 1
hom_alt = 2 (which alt is untracked)
uncalled = None

is_filtered¶: Return True for filtered calls

is_het¶: Return True for filtered calls

is_phased¶: Return True for phased calls

is_variant¶: Return True for filtered calls

phased¶: Return boolean indicating whether this call is phased

plodity = None¶: the number of alleles in this sample’s call

sample = None¶: the name of the sample for which the call was made

site = None¶: the Record of this Call

vcfpy.AltRecord ¶

class vcfpy.AltRecord(type_=None)[source]¶

An alternative allele Record

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

type = None¶: 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, ...