tripal.expression package

Module contents

class tripal.expression.ExpressionClient(tripalinstance, **requestArgs)

Bases: tripal.client.Client

Manage Tripal expressions

add_biomaterial(organism_id, file_path, file_type, analysis_id=None, no_wait=False)

Add a new biomaterial file to the database

Parameters:
  • organism_id (str) – The id of the associated organism
  • analysis_id (str) – The id of the associated analysis. Required for TripalV3
  • file_path (str) – The path to the biomaterial file
  • file_type (str) – The type of the biomaterial file (xml, tsv or csv)
  • no_wait (bool) – Do not wait for job to complete
Return type:

dict
Returns:

Job information
add_expression(organism_id, analysis_id, file_path, match_type=u'uniquename', array_design_id=None, quantification_units=None, file_extension=None, start_regex=None, stop_regex=None, seq_type=None, use_column=False, no_wait=False)

Add an expression file to tripal

Parameters:
  • organism_id (str) – Organism Id
  • analysis_id (str) – Id of the analysis
  • match_type (str) – Match to features using either name or uniquename. Default to uniquename
  • file_path (str) – Path to the expression file, or directory containing multiple expression files
  • array_design_id (str) – The array design ID associated with this analysis. (Non functional in Tripal2)
  • quantification_units (str) – The units associated with the loaded values (ie, FPKM, RPKM, raw counts).
  • file_extension (str) – File extension for the file(s) to be loaded into Chado. Do not include the “.”. Not required for matrix files.
  • start_regex (str) – A regular expression to describe the line that occurs before the start of the expression data. If the file has no header, this is not needed.
  • seq_type (str) – Specify the feature type to associate the data with. (Tripal3 only)
  • stop_regex (str) – A regular expression to describe the line that occurs after the end of the expression data. If the file has no footer text, this is not needed.
  • use_column (bool) – Set if the expression file is a column file
  • no_wait (bool) – Do not wait for job to complete
Return type:

str
Returns:

Loading information
delete_biomaterials(names=[], organism_id=u'', analysis_id=u'', job_name=u'', no_wait=False)

Delete some biomaterials

Parameters:
  • names (str) – JSON list of biomaterial names to delete. (optional)
  • organism_id (str) – Organism id from which to delete biomaterials (optional)
  • analysis_id (str) – Analysis id from which to delete biomaterials (optional)
  • no_wait (bool) – Return immediately without waiting for job completion
  • job_name (str) – Name of the job (optional)
Return type:

str
Returns:

status
get_biomaterials(biomaterial_name=u'', provider_id=u'', biomaterial_id=u'', organism_id=u'', dbxref_id=u'')

List biomaterials in the database

Parameters:
  • organism_id (str) – Limit query to the selected organism
  • biomaterial_id (str) – Limit query to the selected biomaterial
  • biomaterial_name (str) – Limit query to the selected biomaterial
  • provider_id (str) – Limit query to the selected provider
  • dbxref_id (str) – Limit query to the selected ref
Return type:

dict
Returns:

Biomaterial list
get_biomaterials_tripal(biomaterial_id=None)

Get Biomaterial entities

Parameters:biomaterial_id (int) – A biomaterial entity ID
Return type:list of dict
Returns:Organism entity information
sync_biomaterials(ids=u'[]', max_sync=u'', job_name=None, no_wait=False)

Synchronize some biomaterials

Parameters:
  • ids (str) – JSON list of ids of biomaterials to be synced (default: all)
  • max_sync (str) – Maximum number of features to sync (default: all)
  • job_name (str) – Name of the job
  • no_wait (bool) – Return immediately without waiting for job completion
Return type:

str
Returns:

status