feature

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

delete_features command

Usage:

chakin feature delete_features [OPTIONS]

Help

Get all or some features

Output

Features information

Options:

--organism_id INTEGER  organism_id filter
--analysis_id INTEGER  analysis_id filter
--name TEXT            name filter
--uniquename TEXT      uniquename filter
-h, --help             Show this message and exit.

get_feature_analyses command

Usage:

chakin feature get_feature_analyses [OPTIONS] FEATURE_ID

Help

Get analyses associated with a feature

Output

Feature analyses

Options:

-h, --help  Show this message and exit.

get_feature_cvterms command

Usage:

chakin feature get_feature_cvterms [OPTIONS] FEATURE_ID

Help

Get cvterms associated with a feature

Output

Feature cvterms

Options:

-h, --help  Show this message and exit.

get_features command

Usage:

chakin feature get_features [OPTIONS]

Help

Get all or some features

Output

Features information

Options:

--organism_id INTEGER  organism_id filter
--analysis_id INTEGER  analysis_id filter
--name TEXT            name filter
--uniquename TEXT      uniquename filter
-h, --help             Show this message and exit.

load_fasta command

Usage:

chakin feature load_fasta [OPTIONS] FASTA ORGANISM_ID

Help

Load features from a fasta file

Output

Number of inserted sequences

Options:

--sequence_type TEXT    Sequence type  [default: contig]
--analysis_id INTEGER   Analysis ID
--re_name TEXT          Regular expression to extract the feature name from
                        the fasta sequence id (first capturing group will be
                        used).
--re_uniquename TEXT    Regular expression to extract the feature name from
                        the fasta sequence id (first capturing group will be
                        used).
--match_on_name         Match existing features using their name instead of
                        their uniquename
--update                Update existing feature with new sequence instead of
                        throwing an error
--db INTEGER            External database to cross reference to.
--re_db_accession TEXT  Regular expression to extract an external database
                        accession from the fasta sequence id (first capturing
                        group will be used).
--rel_type TEXT         Relation type to parent feature ('part_of' or
                        'derives_from').
--re_parent TEXT        Regular expression to extract parent uniquename from
                        the fasta sequence id (first capturing group will be
                        used).
--parent_type TEXT      Sequence type of the parent feature
-h, --help              Show this message and exit.

load_featureprops command

Usage:

chakin feature load_featureprops [OPTIONS] TAB_FILE ANALYSIS_ID

Help

Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)

Output

Number of inserted featureprop

Options:

--feature_type TEXT  Type of the target features in sequence ontology (will
                     speed up loading if specified)
--match_on_name      Match features using their name instead of their
                     uniquename
-h, --help           Show this message and exit.

load_gff command

Usage:

chakin feature load_gff [OPTIONS] GFF ANALYSIS_ID ORGANISM_ID

Help

Load features from a gff file

Output

None

Options:

--landmark_type TEXT       Type of the landmarks (will speed up loading if
                           provided, e.g. contig, should be a term of the
                           Sequence ontology)
--re_protein TEXT          Replacement string for the protein name using
                           capturing groups defined by --re_protein_capture
--re_protein_capture TEXT  Regular expression to capture groups in mRNA name
                           to use in --re_protein (e.g. "^(.*?)-R([A-Z]+)$",
                           default="^(.*?)$")  [default: ^(.*?)$]
--fasta TEXT               Path to a Fasta containing sequences for some
                           features. When creating a feature, if its sequence
                           is in this fasta file it will be loaded. Otherwise
                           for mRNA and polypeptides it will be computed from
                           the genome sequence (if available), otherwise it
                           will be left empty.
--no_seq_compute           Disable the computation of mRNA and polypeptides
                           sequences based on genome sequence and positions.
--quiet                    Hide progress information
--add_only                 Use this flag if you're not updating existing
                           features, but just adding new features to the
                           selected analysis and organism. It will speedup
                           loading, and reduce memory usage, but might produce
                           errors in case of already existing feature.
--protein_id_attr TEXT     Attribute containing the protein uniquename. It is
                           searched at the mRNA level, and if not found at CDS
                           level.
-h, --help                 Show this message and exit.

load_go command

Usage:

chakin feature load_go [OPTIONS] INPUT ORGANISM_ID ANALYSIS_ID

Help

Load GO annotation from a tabular file

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.