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.