expression

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

add_biomaterial command

Usage:

chakin expression add_biomaterial [OPTIONS] BIOMATERIAL_NAME ORGANISM_ID

Help

Add a new biomaterial to the database

Output

Biomaterial details

Options:

--description TEXT           Description of the biomaterial
--biomaterial_provider TEXT  Biomaterial provider name
--biosample_accession TEXT   Biosample accession number
--sra_accession TEXT         SRA accession number
--bioproject_accession TEXT  Bioproject accession number
--attributes TEXT            Custom attributes (In JSON dict form)
-h, --help                   Show this message and exit.

add_expression command

Usage:

chakin expression add_expression [OPTIONS] ORGANISM_ID ANALYSIS_ID

Help

Add an expression matrix file to the database

Output

Number of expression data loaded

Options:

--separator TEXT   Separating character in the matrix file (ex : ','). Default
                   character is tab.  [default:        ]
--unit TEXT        The units associated with the loaded values (ie, FPKM,
                   RPKM, raw counts)
--query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                   'contig') of the query. It must be a valid Sequence
                   Ontology term.  [default: mRNA]
--match_on_name    Match features using their name instead of their uniquename
--re_name TEXT     Regular expression to extract the feature name from the
                   input file (first capturing group will be used).
--skip_missing     Skip lines with unknown features or GO id instead of
                   aborting everything.
-h, --help         Show this message and exit.

delete_all_biomaterials command

Usage:

chakin expression delete_all_biomaterials [OPTIONS]

Help

Delete all biomaterials

Output

None

Options:

--confirm   Confirm that you really do want to delete ALL of the biomaterials.
-h, --help  Show this message and exit.

delete_biomaterial command

Usage:

chakin expression delete_biomaterial [OPTIONS]

Help

Output

I have no idea

Options:

--names TEXT        JSON list of biomaterial names to delete.  [default: []]
--ids TEXT          JSON list of biomaterial ids to delete.  [default: []]
--organism_id TEXT  Delete all biomaterial associated with this organism id.
--analysis_id TEXT  Delete all biomaterial associated with this analysis id.
-h, --help          Show this message and exit.

delete_biomaterials command

Usage:

chakin expression delete_biomaterials [OPTIONS]

Help

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

Output

Number of deleted biomaterials

Options:

--names TEXT           JSON list of biomaterial names to delete.
--ids TEXT             JSON list of biomaterial ids to delete.
--organism_id INTEGER  Delete all biomaterial associated with this organism
                       id.
--analysis_id INTEGER  Delete all biomaterial associated with this analysis
                       id.
-h, --help             Show this message and exit.

get_biomaterials command

Usage:

chakin expression get_biomaterials [OPTIONS]

Help

List biomaterials in the database

Output

List of biomaterials

Options:

--provider_id INTEGER     Limit query to the selected provider
--biomaterial_id INTEGER  Limit query to the selected biomaterial id
--organism_id INTEGER     Limit query to the selected organism
--biomaterial_name TEXT   Limit query to the selected biomaterial name
--analysis_id INTEGER     Limit query to the selected analysis_id
-h, --help                Show this message and exit.