expression

This section is auto-generated from the help text for the tripaille command expression.

add_biomaterial command

Usage:

tripaille expression add_biomaterial [OPTIONS] ORGANISM_ID FILE_PATH

Help

Add a new biomaterial to the database

Output

Job information

Options:

--no_wait   Do not wait for job to complete
-h, --help  Show this message and exit.

add_expression command

Usage:

tripaille expression add_expression [OPTIONS] ORGANISM_ID ANALYSIS_ID

Help

type organism_id:  str :param organism_id: Organism Id

Output

Loading information

Options:

--match_type TEXT            Match to features using either name or
                             uniquename. Default to uniquename  [default:
                             uniquename]
--biomaterial_provider TEXT  The contact who provided the biomaterial.
                             (optional, non functional in Tripal2)
--array_design TEXT          The array design associated with this analysis.
                             This is not required if the experimental data was
                             gathered from next generation sequencing methods.
                             (optional, non functional in Tripal2)
--assay_id TEXT              The id of the assay associated with the
                             experiment. (optional, non functional in Tripal2)
--acquisition_id TEXT        The id of the acquisition associated with the
                             experiment (optional, non functional in Tripal2)
--quantification_id TEXT     The id of the quantification associated with the
                             experiment (optional, non functional in Tripal2)
--file_extension TEXT        File extension for the file(s) to be loaded into
                             Chado. Do not include the ".". Not required for
                             matrix files. (optional)
--start_regex TEXT           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.
                             (optional)
--stop_regex TEXT            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.
                             (optional)
--use_column                 Set if the expression file is a column file
--no_wait                    Do not wait for job to complete
-h, --help                   Show this message and exit.

delete_biomaterials command

Usage:

tripaille expression delete_biomaterials [OPTIONS]

Help

Delete some biomaterials

Output

status

Options:

--names TEXT        JSON list of biomaterial names to delete. (optional)
--organism_id TEXT  Organism id from which to delete biomaterials (optional)
--analysis_id TEXT  Analysis id from which to delete biomaterials (optional)
--job_name TEXT     Name of the job (optional)
--no_wait           Return immediately without waiting for job completion
-h, --help          Show this message and exit.

get_biomaterials command

Usage:

tripaille expression get_biomaterials [OPTIONS]

Help

List biomaterials in the database

Output

Job information

Options:

--provider_id TEXT     Limit query to the selected provider
--biomaterial_id TEXT  Limit query to the selected biomaterial
--organism_id TEXT     Limit query to the selected organism
--dbxref_id TEXT       Limit query to the selected ref
-h, --help             Show this message and exit.

sync_biomaterials command

Usage:

tripaille expression sync_biomaterials [OPTIONS]

Help

Synchronize some biomaterials

Output

status

Options:

--ids TEXT       JSON list of ids of biomaterials to be synced (default: all)
--max_sync TEXT  Maximum number of features to sync (default: all)
--job_name TEXT  Name of the job
--no_wait        Return immediately without waiting for job completion
-h, --help       Show this message and exit.