lookups

Lookups for a PostgreSQL database with genomic data.

Lookup functions for the variant browser.

autocomplete(dataset: str, query: str, ds_version: str = None)

Provide autocomplete suggestions based on the query.

Parameters:

• dataset (str) – short name of dataset
• query (str) – the query to compare to the available gene names
• ds_version (str) – the dataset version

Returns:

A list of genes names whose beginning matches the query

Return type:

list

get_awesomebar_result(dataset: str, query: str, ds_version: str = None)

Parse the search input.

Datatype is one of:

• gene
• transcript
• variant
• dbsnp_variant_set
• region

Identifier is one of:

• ensembl ID for gene
• variant ID string for variant (eg. 1-1000-A-T)
• region ID string for region (eg. 1-1000-2000)

Follow these steps:

• if query is an ensembl ID, return it
• if a gene symbol, return that gene’s ensembl ID
• if an RSID, return that variant’s string

Parameters:

• dataset (str) – short name of dataset
• query (str) – the search query
• ds_version (str) – the dataset version

Returns:

(datatype, identifier)

Return type:

tuple

get_coverage_for_bases(dataset: str, chrom: str, start_pos: int, end_pos: int = None, ds_version: str = None)

Get the coverage for the list of bases given by start_pos->end_pos, inclusive.

Parameters:

• dataset (str) – short name for the dataset
• chrom (str) – chromosome
• start_pos (int) – first position of interest
• end_pos (int) – last position of interest; if None it will be set to start_pos
• ds_version (str) – version of the dataset

Returns:

coverage dicts for the region of interest. None if failed

Return type:

list

get_coverage_for_transcript(dataset: str, chrom: str, start_pos: int, end_pos: int = None, ds_version: str = None)

Get the coverage for the list of bases given by start_pos->end_pos, inclusive.

Parameters:

• dataset (str) – short name for the dataset
• chrom (str) – chromosome
• start_pos (int) – first position of interest
• end_pos (int) – last position of interest; if None it will be set to start_pos
• ds_version (str) – version of the dataset

Returns:

coverage dicts for the region of interest

Return type:

list

get_exons_in_transcript(dataset: str, transcript_id: str, ds_version=None)

Retrieve exons associated with the given transcript id.

Parameters:

• dataset (str) – short name of the dataset
• transcript_id (str) – the id of the transcript
• ds_version (str) – dataset version

Returns:

dicts with values for each exon sorted by start position

Return type:

list

get_gene(dataset: str, gene_id: str, ds_version: str = None)

Retrieve gene by gene id.

Parameters:

• dataset (str) – short name of the dataset
• gene_id (str) – the id of the gene
• ds_version (str) – dataset version

Returns:

values for the gene; None if not found

Return type:

dict

get_gene_by_dbid(gene_dbid: str)

Retrieve gene by gene database id.

Parameters:gene_dbid (str) – the database id of the gene Returns:values for the gene; empty if not found Return type:dict

get_gene_by_name(dataset: str, gene_name: str, ds_version=None)

Retrieve gene by gene_name.

Parameters:

• dataset (str) – short name of the dataset
• gene_name (str) – the id of the gene
• ds_version (str) – dataset version

Returns:

values for the gene; empty if not found

Return type:

dict

get_genes_in_region(dataset: str, chrom: str, start_pos: int, stop_pos: int, ds_version: str = None)

Retrieve genes located within a region.

Parameters:

• dataset (str) – short name of the dataset
• chrom (str) – chromosome name
• start_pos (int) – start of region
• stop_pos (int) – end of region
• ds_version (str) – dataset version

Returns:

values for the gene; empty if not found

Return type:

dict

get_raw_variant(dataset: str, pos: int, chrom: str, ref: str, alt: str, ds_version: str = None)

Retrieve variant by position and change.

Parameters:

• dataset (str) – short name of the reference set
• pos (int) – position of the variant
• chrom (str) – name of the chromosome
• ref (str) – reference sequence
• alt (str) – variant sequence
• ds_version (str) – dataset version

Returns:

values for the variant; None if not found

Return type:

dict

get_transcript(dataset: str, transcript_id: str, ds_version: str = None)

Retrieve transcript by transcript id.

Also includes exons as [‘exons’]

Parameters:

• dataset (str) – short name of the dataset
• transcript_id (str) – the id of the transcript
• ds_version (str) – dataset version

Returns:

values for the transcript, including exons; None if not found

Return type:

dict

get_transcripts_in_gene(dataset: str, gene_id: str, ds_version: str = None)

Get the transcripts associated with a gene.

Parameters:

• dataset (str) – short name of the reference set
• gene_id (str) – id of the gene
• ds_version (str) – dataset version

Returns:

transcripts (dict) associated with the gene; empty if no hits

Return type:

list

get_transcripts_in_gene_by_dbid(gene_dbid: int)

Get the transcripts associated with a gene.

Parameters:gene_dbid (int) – database id of the gene Returns:transcripts (dict) associated with the gene; empty if no hits Return type:list

get_variant(dataset: str, pos: int, chrom: str, ref: str, alt: str, ds_version: str = None)

Retrieve variant by position and change.

Parameters:

• dataset (str) – short name of the dataset
• pos (int) – position of the variant
• chrom (str) – name of the chromosome
• ref (str) – reference sequence
• alt (str) – variant sequence
• ds_version (str) – version of the dataset

Returns:

values for the variant; None if not found

Return type:

dict

get_variants_by_rsid(dataset: str, rsid: str, ds_version: str = None)

Retrieve variants by their associated rsid.

Parameters:

• dataset (str) – short name of dataset
• rsid (str) – rsid of the variant (starting with rs)
• ds_version (str) – version of the dataset

Returns:

variants as dict; no hits returns None

Return type:

list

get_variants_in_gene(dataset: str, gene_id: str, ds_version: str = None)

Retrieve variants present inside a gene.

Parameters:

• dataset (str) – short name of the dataset
• gene_id (str) – id of the gene
• ds_version (str) – version of the dataset

Returns:

values for the variants

Return type:

list

get_variants_in_region(dataset: str, chrom: str, start_pos: int, end_pos: int, ds_version: str = None)

Variants that overlap a region.

Parameters:

• dataset (str) – short name of the dataset
• chrom (str) – name of the chromosom
• start_pos (int) – start of the region
• end_pos (int) – start of the region
• ds_version (str) – version of the dataset

Returns:

variant dicts, None if no hits

Return type:

list

get_variants_in_transcript(dataset: str, transcript_id: str, ds_version: str = None)

Retrieve variants inside a transcript.

Parameters:

• dataset (str) – short name of the dataset
• transcript_id (str) – id of the transcript (ENST)
• ds_version (str) – version of the dataset

Returns:

values for the variant; None if not found

Return type:

dict