variants package¶

Variants in families¶

Example usage of `variants`¶

Example usage of variants package:

import os
from utils.variant_utils import mat2str
from variants.builder import variants_builder as VB

prefix = "ivan-tiny/a"
# prefix = "spark/nspark"
prefix = 'fixtures/effects_trio'

genome_file = os.path.join(
    os.environ.get("DAE_DB_DIR"),
    "genomes/GATK_ResourceBundle_5777_b37_phiX174",
    "chrAll.fa")
print(genome_file)

gene_models_file = os.path.join(
    os.environ.get("DAE_DB_DIR"),
    "genomes/GATK_ResourceBundle_5777_b37_phiX174",
    "refGene-201309.gz")
print(gene_models_file)


fvars = VB(prefix=prefix, genome_file=genome_file,
           gene_models_file=gene_models_file)

vs = fvars.query_variants()


for c, v in enumerate(vs):
    print(c, v, v.family_id, mat2str(v.best_st), sep='\t')
    for aa in v.alt_alleles:
        print(aa.effect.worst, aa.effect.genes)
        print(aa['af_allele_count'], aa['af_allele_freq'])

Family variants query interface¶

Once you have family variants interface created, you can use it to search for variants you are interested in. The variants interface supports query by various attributes of the family variants:

query by genome regions

query by genes and variant effect types

query by inheritance types

query by family IDs

query by person IDs

query by sexes

query by family roles

query by variant types

query by real value variant attributes (scores).

query using general purpose filter function

In the following examples we will assume that fvars is an instance of family variants query interface that allows searching for variants by various criteria.

Query by regions¶

The query interface support searching of variants in given genome region or list of regions.

Example

The following example will return variants that are at one single position on chromosome 1:878109:

from RegionOperations import Region

vs = fvars.query_variants(regions=[Region("1", 878109, 878109)])

You can specify list of regions in the query:

from RegionOperations import Region

vs = fvars.query_variants(
    regions=[Region("1", 11539, 11539), Region("1", 11550, 11550)])

Query by genes and effect types¶

Example

The following example will return only variants with effect type frame-shift:

vs = fvars.query_variants(
    effects=["frame-shift"])

You can specify multiple effects in the query. The following example will return variants that with effect type frame-shift or missense:

vs = fvars.query_variants(
    effects=["frame-shift", "missense"])

You can search for variants in specific gene:

vs = fvars.query_variants(
    genes=["PLEKHN1"])

or list of genes:

vs = fvars.query_variants(
    genes=["PLEKHN1", "SAMD11"])

You can specifye combination of effect types and genes in which case the query will return only variants that match both criteria:

vs = fvars.query_variants(
    effect_types=["synonymous", "frame-shift"],
    genes=["PLEKHN1"])

Query by inheritance¶

Example

The following example will return only variants that have inheritance type denovo:

vs = fvars.query_variants(
    inheritance="denovo")

You can inheritance type using or:

vs = fvars.query_variants(
    inheritance="denovo or omission")

You can use not to get all family variants that has non reference inheritance type:

vs = fvars.query_variants(inheritance="not reference")

Query by family IDs¶

Example

The following example will return only variants that affect specified families:

vs = fvars.query_variants(family_ids=['f1', 'f2'])

where f1 and f2 are family IDs.

Query by person IDs¶

Example

The following example will return only variants that affect specified individuals:

vs = fvars.query_variants(person_ids=['mom2', 'ch2'])

where mom2 and ch2 are persons (individuals) IDs.

Query by sexes¶

Example

The following example will return only variants that affect male individuals:

vs = fvars.query_variants(sexes="male")

You can use or to combine sexes and not to negate. For example:

vs = fvars.query_variants(sexes="male and not female")

will return only family variants that affect male individuals in family, but not female.

Query by roles¶

Example

The following example will return only variants that affect probands in families:

vs = fvars.query_variants(roles="prb")

You can use or, and and not to combine roles. For example:

vs = fvars.query_variants(roles="prb and not sib")

will return only family variants that affect probands in family, but not siblings.

Query by variant types¶

Example

The following example will return only variants that are of type sub:

vs = fvars.query_variants(variant_types="sub")

You can use or, and and not to combine variant types. For example:

vs = fvars.query_variants(roles="sub or del")

will return only family variants that are of type sub or del.

Query with real value variant attributes (scores)¶

Not fully implemented yet

Query with filter function¶

Not fully implemented yet

VariantBase - a base class for variants¶

SummaryAllele - a base class for representing alleles¶

class dae.variants.variant.SummaryAllele(chromosome: str, position: int, reference: str, alternative: Optional[str] = None, summary_index: int = -1, allele_index: int = 0, transmission_type: dae.variants.attributes.TransmissionType = <TransmissionType.transmitted: 1>, attributes: Dict[str, Any] = None)[source]¶

SummaryAllele represents a single allele for given position.

__init__(chromosome: str, position: int, reference: str, alternative: Optional[str] = None, summary_index: int = -1, allele_index: int = 0, transmission_type: dae.variants.attributes.TransmissionType = <TransmissionType.transmitted: 1>, attributes: Dict[str, Any] = None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

property allele_index¶: index of the allele in summary variant

property alternative¶

property attributes¶: additional attributes of the allele

property chrom¶

property chromosome¶

static create_reference_allele(allele) → dae.variants.variant.Allele[source]¶

property cshl_location¶

property cshl_position¶

property cshl_variant¶

property details¶

property effect¶: effects of the allele; None for the reference allele.

property effects¶

property frequency¶

get_attribute(item: str, default=None)¶: looks up values matching key item in additional attributes passed on creation of the variant.

has_attribute(item: str) → bool¶: checks if additional variant attributes contain values for key item.

property is_reference_allele¶

property position¶

property reference¶

property summary_index¶: index of the summary variant this allele belongs to

property transmission_type¶

update_attributes(atts) → None¶: updates additional attributes of variant using dictionary atts.

property variant_type¶

SummaryVariant - representation of summary variants¶

class dae.variants.variant.SummaryVariant(alleles)[source]¶

__contains__(item: Any) → bool¶

__getitem__(item: Any) → List[any]¶

__init__(alleles)[source]¶: Initialize self. See help(type(self)) for accurate signature.

property allele_count¶

property alleles¶: list of all alleles of the variant

property alt_alleles¶: list of all alternative alleles

property alternative¶

property chrom¶

property chromosome¶

property details¶: 1-based list of VariantDetails, that describes each alternative allele.

property effects¶: 1-based list of Effect, that describes variant effects.

property frequencies¶: 0-base list of frequencies for variant.

get_attribute(item: Any, default: Optional[Any] = None) → List[Any]¶

has_attribute(item: Any) → bool¶

property location¶

property position¶

property ref_allele¶: the reference allele

property reference¶

property summary_index¶

update_attributes(atts: Dict[str, Any]) → None¶

property variant¶

property variant_types¶: returns set of variant types.

FamilyDelegate - common inheritance methods¶

class dae.variants.family_variant.FamilyDelegate(family)[source]¶

property family_id¶: Returns the family ID.

property members_ids¶: Returns list of family members IDs.

property members_in_order¶: Returns list of the members of the family in the order specified from the pedigree file. Each element of the returned list is an object of type variants.family.Person.

FamilyAllele - representation of family allele¶

class dae.variants.family_variant.FamilyAllele(summary_allele: dae.variants.variant.SummaryAllele, family: dae.pedigrees.family.Family, genotype, best_state, genetic_model=None, inheritance_in_members=None)[source]¶

property allele_index¶: index of the allele in summary variant

property alternative¶

property attributes¶: additional attributes of the allele

best_st()¶: Deprecated since version Replace: best_st with best_state

property best_state¶

classmethod calc_inheritance_trio(p1, p2, ch, allele_index)[source]¶

Calculates the inheritance type of a trio family.

Parameters

p1 – genotype of the first parent (pair of allele indexes).
p2 – genotype of the second parent.
ch – genotype of the child.

Returns

inheritance type as variants.attributes.Inheritance of the trio family.

static check_denovo_trio(p1, p2, ch, allele_index)[source]¶

Checks if the inheritance type for a trio family is denovo.

Parameters

p1 – genotype of the first parent (pair of allele indexes).
p2 – genotype of the second parent.
ch – genotype of the child.

Returns

True, when the inheritance is mendelian.

static check_mendelian_trio(p1, p2, ch, allele_index)[source]¶

Checks if the inheritance type for a trio family is mendelian.

Parameters

p1 – genotype of the first parent (pair of allele indexes).
p2 – genotype of the second parent.
ch – genotype of the child.

Returns

True, when the inheritance is mendelian.

static check_omission_trio(p1, p2, ch, allele_index)[source]¶

Checks if the inheritance type for a trio family is omission.

Parameters

p1 – genotype of the first parent (pair of allele indexes).
p2 – genotype of the second parent.
ch – genotype of the child.

Returns

True, when the inheritance is mendelian.

property chrom¶

property chromosome¶

property cshl_location¶

property cshl_position¶

property cshl_variant¶

property details¶

property effect¶: effects of the allele; None for the reference allele.

property effects¶

property family_id¶: Returns the family ID.

property frequency¶

property genetic_model¶

property genotype¶: Returns genotype of the family.

get_attribute(item: str, default=None)¶: looks up values matching key item in additional attributes passed on creation of the variant.

gt_flatten()[source]¶: Return genotype of the family variant flattened to 1-dimensional array.

has_attribute(item: str) → bool¶: checks if additional variant attributes contain values for key item.

property inheritance_in_members¶

property is_reference_allele¶

property members_ids¶: Returns list of family members IDs.

property members_in_order¶: Returns list of the members of the family in the order specified from the pedigree file. Each element of the returned list is an object of type variants.family.Person.

property position¶

property reference¶

summary_allele = None¶: summary allele that corresponds to this allele in family variant

property summary_index¶: index of the summary variant this allele belongs to

property transmission_type¶

update_attributes(atts) → None¶: updates additional attributes of variant using dictionary atts.

property variant_in_members¶: Returns set of members IDs of the family that are affected by this family variant.

property variant_in_members_objects¶

property variant_in_roles¶: Returns list of roles (or ‘None’) of the members of the family that are affected by this family variant.

property variant_in_sexes¶: Returns list of sexes (or ‘None’) of the members of the family that are affected by this family variant.

property variant_type¶

FamilyVariant - representation of family variants¶

class dae.variants.family_variant.FamilyVariant(summary_variant: dae.variants.variant.SummaryVariant, family: dae.pedigrees.family.Family, genotype: Any, best_state: Any)[source]¶

property allele_count¶

property alleles¶: list of all alleles of the variant

property alt_alleles¶: list of all alternative alleles

property alternative¶

property best_st¶: Deprecated since version Replace: usage of best_st with best_state

property best_state¶

static calc_alleles(gt)[source]¶

Returns allele indexes that are relevant for the given genotype.

Parameters: gt – genotype as np.array.
Returns: list of all allele indexes present into genotype passed.

static calc_alt_alleles(gt)[source]¶

Returns alternative allele indexes that are relevant for the given genotype.

Parameters: gt – genotype as np.array.
Returns: list of all alternative allele indexes present into genotype passed.

property chrom¶

property chromosome¶

property details¶: 1-based list of VariantDetails, that describes each alternative allele.

property effects¶: 1-based list of Effect, that describes variant effects.

property family_id¶: Returns the family ID.

property frequencies¶: 0-base list of frequencies for variant.

property fvuid¶

property genetic_model¶

property genotype¶: Returns genotype of the family.

get_attribute(item: Any, default: Optional[Any] = None) → List[Any]¶

gt_flatten()[source]¶: Return genotype of the family variant flattened to 1-dimensional array.

has_attribute(item: Any) → bool¶

is_reference()[source]¶: Returns True if all known alleles in the family variant are reference.

is_unknown()[source]¶: Returns True if all alleles in the family variant are unknown.

property location¶

property matched_alleles¶

property matched_alleles_indexes¶

property matched_gene_effects¶

property members_ids¶: Returns list of family members IDs.

property members_in_order¶: Returns list of the members of the family in the order specified from the pedigree file. Each element of the returned list is an object of type variants.family.Person.

property position¶

property ref_allele¶: the reference allele

property reference¶

set_matched_alleles(alleles_indexes)[source]¶

property summary_index¶

update_attributes(atts: Dict[str, Any]) → None¶

property variant¶

property variant_types¶: returns set of variant types.

RawVcfVariants - query interface for VCF variants¶

Apache Parquet variants schema¶

Summary Variants/Alleles flat schema¶

chrom (string) -
chromosome where variant is located
position (int64) -
1-based position of the start of the variant
reference (string) -
reference DNA string
alternative (string) -
alternative DNA string (None for reference allele)
summary_index (int64) -
index of the summary variant
allele_index (int16) -
index of the allele inside given summary variant
variant_type (int8) -
variant type in CSHL nottation
cshl_variant (string) -
variant description in CSHL notation
cshl_position (int64) -
variant position in CSHL notation
cshl_length (int32) -
variant length in CSHL notation
effect_type (string) -
worst effect of the variant (None for reference allele)
effect_gene_genes (list_(string)) -
list of all genes affected by the variant allele (None for reference allele)
effect_gene_types (list_(string)) -
list of all effect types corresponding to the effect_gene_genes (None for reference allele)
effect_details_transcript_ids (list_(string)) -
list of all transcript ids affected by the variant allele (None for reference allele)
effect_details_details (list_(string)) -
list of all effected details corresponding to the effect_details_transcript_ids (None for reference allele)
af_parents_called_count (int32) -
count of independent parents that has well specified genotype for this allele
af_parents_called_percent (float64) -
parcent of independent parents corresponding to af_parents_called_count
af_allele_count (int32) -
count of this allele in the independent parents
af_allele_freq (float64) -
allele frequency

Family Variants schema¶

chrom (string)
position (int64)
family_index (int64) -
index of the family variant
summary_index (int64) -
index of the summary variant
family_id (string) -
family ID
genotype (list_(int8)) -
genotype of the variant for the specified family
inheritance (int32) -
inheritance type of the variant

Family Alleles schema¶

family_index (int64)
summary_index (int64)
allele_index (int16)
variant_in_members (list_(string)) -
list of members of the family that have this allele
variant_in_roles (list_(int32)) -
list of family members’ roles that have this allele
variant_in_sexes (list_(int8)) -
list of family members’ sexes that have this allele

Variant Scores schema¶

summary_index (int64)
allele_index (int16)
score_id (string or int64)
score_value (float64)

Pedigree file schema¶

familyId (string)
personId (string)
dadId (string)
momId (string)
sex (int8)
status (int8)
role (int32)
sampleId (string)
order (int32)

variants package¶

Variants in families¶

Example usage of variants¶

Family variants query interface¶

Query by regions¶

Query by genes and effect types¶

Query by inheritance¶

Query by family IDs¶

Query by person IDs¶

Query by sexes¶

Query by roles¶

Query by variant types¶

Query with real value variant attributes (scores)¶

Query with filter function¶

VariantBase - a base class for variants¶

SummaryAllele - a base class for representing alleles¶

SummaryVariant - representation of summary variants¶

FamilyDelegate - common inheritance methods¶

FamilyAllele - representation of family allele¶

FamilyVariant - representation of family variants¶

RawVcfVariants - query interface for VCF variants¶

Apache Parquet variants schema¶

Summary Variants/Alleles flat schema¶

Family Variants schema¶

Family Alleles schema¶

Variant Scores schema¶

Pedigree file schema¶

Functions from parquet_io module¶

Example usage of `variants`¶