load

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

blast command

Usage:

chakin load blast [OPTIONS] ANALYSIS_ID ORGANISM_ID INPUT

Help

Load a blast analysis, in the same way as does the tripal_analysis_blast module

Output

Number of processed hits

Options:

--blastdb TEXT        Name of the database blasted against (must be in the
                      Chado db table)
--blastdb_id INTEGER  ID of the database blasted against (must be in the Chado
                      db table)
--re_name TEXT        Regular expression to extract the feature name from the
                      input file (first capturing group will be used).
--query_type TEXT     The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                      'contig') of the query. It must be a valid Sequence
                      Ontology term.  [default: polypeptide]
--match_on_name       Match features using their name instead of their
                      uniquename
--skip_missing        Skip lines with unknown features or GO id instead of
                      aborting everything.
-h, --help            Show this message and exit.

go command

Usage:

chakin load go [OPTIONS] INPUT ORGANISM_ID ANALYSIS_ID

Help

Load GO annotation from a tabular file, in the same way as does the tripal_analysis_go module

Output

Number of inserted GO terms

Options:

--query_type TEXT      The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                       'contig') of the query. It must be a valid Sequence
                       Ontology term.  [default: polypeptide]
--match_on_name        Match features using their name instead of their
                       uniquename
--name_column INTEGER  Column containing the feature identifiers (2, 3, 10 or
                       11; default=2).  [default: 2]
--go_column INTEGER    Column containing the GO id (default=5).  [default: 5]
--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.

interpro command

Usage:

chakin load interpro [OPTIONS] ANALYSIS_ID ORGANISM_ID INPUT

Help

Load an InterProScan analysis, in the same way as does the tripal_analysis_intepro module

Output

Number of processed hits

Options:

--parse_go         Load GO annotation to the database
--re_name TEXT     Regular expression to extract the feature name from the
                   input file (first capturing group will be used).
--query_type TEXT  The feature type (e.g. 'gene', 'mRNA', 'polypeptide',
                   'contig') of the query. It must be a valid Sequence
                   Ontology term.  [default: polypeptide]
--match_on_name    Match features using their name instead of their uniquename
--skip_missing     Skip lines with unknown features or GO id instead of
                   aborting everything.
-h, --help         Show this message and exit.