4.1.1.1.1.1.1.6. datanator.api.lib.subunit package

4.1.1.1.1.1.1.6.1. Submodules

4.1.1.1.1.1.1.6.2. datanator.api.lib.subunit.manager module

Author:Saahith Pochiraju <saahith116@gmail.com>
Date:2018-08-20
Copyright:2017, Karr Lab
License:MIT
class datanator.api.lib.subunit.manager.ProteinSubunitManager(cache_dirname='/root/.wc/data/datanator')[source]

Bases: datanator.api.lib.data_manager.BaseManager

Manages subunit information for API

get_abundance_by_gene_name(gene_name, select=<class 'datanator.core.models.AbundanceData'>)[source]

Find the abundance from gene_name

Parameters:gene_name (str) – gene name for a given protein
Returns:query for matching abundance rows
Return type:sqlalchemy.orm.query.Query
get_abundance_by_length(length, select=<class 'datanator.core.models.AbundanceData'>)[source]

Find the abundance from uniprot

Parameters:length (str) – number of amino acids in a protein
Returns:query for matching abundance rows
Return type:sqlalchemy.orm.query.Query
get_abundance_by_mass(mass, select=<class 'datanator.core.models.AbundanceData'>)[source]

Find the abundance from uniprot

Parameters:mass (int) – mass of a protein
Returns:query for matching abundance rows
Return type:sqlalchemy.orm.query.Query
get_abundance_by_sequence(sequence, select=<class 'datanator.core.models.AbundanceData'>)[source]

Find the abundance from uniprot

Parameters:sequence (str) – amino acid sequence for a given protein
Returns:query for matching abundance rows
Return type:sqlalchemy.orm.query.Query
get_abundance_by_uniprot(uniprot, select=<class 'datanator.core.models.AbundanceData'>)[source]

Find the abundance from a uniprot id

Parameters:uniprot (str) – protein id from Uniprot Database
Returns:query for matching abundance rows
Return type:sqlalchemy.orm.query.Query
get_interaction_by_subunit(uniprot, select=<class 'datanator.core.models.ProteinInteraction'>)[source]

Get interactions that were observed for a given uniprot id

Parameters:uniprot (str) – uniprot id to search for
Returns:query for protein interactions that contain the uniprot_id
Return type:sqlalchemy.orm.query.Query
get_known_complex_by_subunit(uniprot, select=<class 'datanator.core.models.ProteinComplex'>)[source]

Get known complexes that were observed for a given uniprot id subunit

Parameters:uniprot (str) – uniprot id to search for
Returns:query for protein complexes that contain the uniprot_id
Return type:sqlalchemy.orm.query.Query
get_observable_complex(protein_subunit)[source]

Get known protein complex that were observed for a given subunit

Parameters:protein_subunit (models.ProteinSubunit) – subunit to find complex for
Returns:list of Protein Complexes
Return type:list of data_model.ObservedSpecie
get_observable_interactions(protein_subunit)[source]

Get known protein interactions that were observed for a given subunit

Parameters:protein_subunit (models.ProteinSubunit) – subunit to find interactions for
Returns:list of Observed Protein Interactions
Return type:list of data_model.ObservedInteraction
get_observed_abundances(protein)[source]

Find the observed values for protein abundance

Parameters:protein (models.ProteinSubunit) – Protein Subunit to find data for
Returns:list of relevant observed values
Return type:list of data_model.ObservedValue
get_subunit_by_id(id)[source]

4.1.1.1.1.1.1.6.3. Module contents