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.