biggr_models.queries.gene_queries#

Attributes#

NON_LINK_SOURCES

Functions#

`get_database_links_for_gene`(→ Dict[str, list])	Collect this gene's cross-references, grouped by source database.
`get_gene_ids_for_gene_name`(name, session)	Get the gene ids for a gene name.
`get_genes`(gene_ids, session)	Get the genes for a list of gene ids.
`get_all_genes`(session)	Get all genes.
`get_all_genes_with_urls`(session[, after, limit])	Get all genes with URLs, cursor-based pagination.
`get_all_gene_strain_pairs`(session[, after, limit])	Get all gene-strain pairs, one row per (gene, strain, bigg_id). Cursor-based pagination.
`get_genes_with_genome_region`(gene_ids, session)	Get gene + genome_region flattened data with genome_gene_url for a list of gene IDs.
`get_model_genes_for_gene_ids`(gene_ids, session)	Get model_gene + model flattened data with model_gene_url for a list of gene IDs.
`get_urls_for_gene_ids`(gene_ids, session)	Get genome and model URLs for a list of gene IDs, grouped by gene ID.
`get_genome_region_for_gene_id`(ids, session)	Get the genome region for a gene id.
`get_model_genes_count`(model_bigg_id, session)	Get the number of gene for the given model.
`get_model_genes`(model_bigg_id, session[, page, size, ...])	Get model genes.
`get_model_gene`(gene_bigg_id, model_bigg_id, session)
`get_gene`(→ Dict[str, Any])

Module Contents#

biggr_models.queries.gene_queries.NON_LINK_SOURCES#

biggr_models.queries.gene_queries.get_database_links_for_gene(session: sqlalchemy.orm.Session, gene_db_id: int) → Dict[str, list]#

Collect this gene’s cross-references, grouped by source database.

The ETL already stores every /db_xref from the GenBank file as a synonym, so this is a read of data that is loaded but was never surfaced. Sources that merely restate the gene’s own names are skipped, and a source with no url_prefix yields text rather than a link.

biggr_models.queries.gene_queries.get_gene_ids_for_gene_name(name, session)#: Get the gene ids for a gene name.

biggr_models.queries.gene_queries.get_genes(gene_ids, session)#: Get the genes for a list of gene ids.

biggr_models.queries.gene_queries.get_all_genes(session)#: Get all genes.

biggr_models.queries.gene_queries.get_all_genes_with_urls(session, after=None, limit=100000)#

Get all genes with URLs, cursor-based pagination.

Uses a single opaque cursor that encodes the internal two-phase state (genome genes first, then model genes).

Cursor format: “g:<Gene.id>” for genome phase, “m:<ModelGene.id>” for model phase.

biggr_models.queries.gene_queries.get_all_gene_strain_pairs(session, after=None, limit=100000)#: Get all gene-strain pairs, one row per (gene, strain, bigg_id). Cursor-based pagination.

biggr_models.queries.gene_queries.get_genes_with_genome_region(gene_ids, session)#: Get gene + genome_region flattened data with genome_gene_url for a list of gene IDs.

biggr_models.queries.gene_queries.get_model_genes_for_gene_ids(gene_ids, session)#: Get model_gene + model flattened data with model_gene_url for a list of gene IDs.

biggr_models.queries.gene_queries.get_urls_for_gene_ids(gene_ids, session)#: Get genome and model URLs for a list of gene IDs, grouped by gene ID.

biggr_models.queries.gene_queries.get_genome_region_for_gene_id(ids, session)#: Get the genome region for a gene id.

biggr_models.queries.gene_queries.get_model_genes_count(model_bigg_id, session)#: Get the number of gene for the given model.

biggr_models.queries.gene_queries.get_model_genes(model_bigg_id, session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)#

Get model genes.

Parameters:

model_bigg_id (The bigg id of the model to retrieve genes.)
session (An ome session object.)
page (The page, or None for all pages.)
size (The page length, or None for all pages.)
sort_column (The name of the column to sort. Must be one of 'bigg_id', 'name',)
'model_bigg_id'
'organism'. (and)
sort_direction (Either 'ascending' or 'descending'.)

Returns:

A list of objects with keys ‘bigg_id’, ‘name’, ‘model_bigg_id’, and
’organism’.

biggr_models.queries.gene_queries.get_model_gene(gene_bigg_id, model_bigg_id, session)#

biggr_models.queries.gene_queries.get_gene(session: sqlalchemy.orm.Session, accession_type: str, accession_value: str, gene_bigg_id: str) → Dict[str, Any]#