chado.expression package

Module contents

Contains possible interactions with the Chado base for expressions and biomaterials

class chado.expression.ExpressionClient(engine, metadata, session, ci)

Bases: chado.client.Client

Interact with expressions

add_biomaterial(biomaterial_name, organism_id, description='', biomaterial_provider='', biosample_accession='', sra_accession='', bioproject_accession='', attributes={})

Add a new biomaterial to the database

Parameters:
  • biomaterial_name (str) – Biomaterial name
  • organism_id (int) – The id of the associated organism
  • description (str) – Description of the biomaterial
  • biomaterial_provider (str) – Biomaterial provider name
  • biosample_accession (str) – Biosample accession number
  • sra_accession (str) – SRA accession number
  • bioproject_accession (str) – Bioproject accession number
  • attributes (str) – Custom attributes (In JSON dict form)
Return type:

dict
Returns:

Biomaterial details
add_expression(organism_id, analysis_id, file_path, separator='\t', unit=None, query_type='mRNA', match_on_name=False, re_name=None, skip_missing=False)

Add an expression matrix file to the database

Parameters:
  • organism_id (int) – The id of the associated organism
  • analysis_id (int) – The id of the associated analysis
  • file_path (str) – File path
  • separator (str) – Separating character in the matrix file (ex : ‘,’). Default character is tab.
  • unit (str) – The units associated with the loaded values (ie, FPKM, RPKM, raw counts)
  • query_type (str) – The feature type (e.g. ‘gene’, ‘mRNA’, ‘polypeptide’, ‘contig’) of the query. It must be a valid Sequence Ontology term.
  • match_on_name (bool) – Match features using their name instead of their uniquename
  • re_name (str) – Regular expression to extract the feature name from the input file (first capturing group will be used).
  • skip_missing (bool) – Skip lines with unknown features or GO id instead of aborting everything.
Return type:

str
Returns:

Number of expression data loaded
delete_all_biomaterials(confirm=False)

Delete all biomaterials

Parameters:confirm (bool) – Confirm that you really do want to delete ALL of the biomaterials.
Return type:None
Returns:None
delete_biomaterials(names=None, ids=None, organism_id='', analysis_id='')

Will delete biomaterials based on selector. Only one selector will be used.

Parameters:
  • names (str) – JSON list of biomaterial names to delete.
  • ids (str) – JSON list of biomaterial ids to delete.
  • organism_id (int) – Delete all biomaterial associated with this organism id.
  • analysis_id (int) – Delete all biomaterial associated with this analysis id.
Return type:

str
Returns:

Number of deleted biomaterials
get_biomaterials(provider_id='', biomaterial_id='', organism_id='', biomaterial_name='', analysis_id='')

List biomaterials in the database

Parameters:
  • organism_id (int) – Limit query to the selected organism
  • biomaterial_id (int) – Limit query to the selected biomaterial id
  • provider_id (int) – Limit query to the selected provider
  • biomaterial_name (str) – Limit query to the selected biomaterial name
  • analysis_id (int) – Limit query to the selected analysis_id
Return type:

list
Returns:

List of biomaterials