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.