domainator filter_domains
Filter domain annotations by e-value, overlap, database, or name.
Filter domain anntations
Takes a genbank file which has been annotated through the domainator program and filters domainator annotations,
based on percentage overlap between domains and evalues of domains.
Give at least one of these outputs: --genbank_out, --fasta_out. - as an input or output means standard input or output, where the option says it is allowed.
| Option | Value | Default | Description |
|---|---|---|---|
-v, --verbose |
show debug output, and a traceback for errors. | ||
-q, --quiet |
show errors only: no progress messages or warnings. | ||
-i, --input |
FILE ... | required | The genbank filenames to be filtered. Use - to read standard input. |
-o, --genbank_out |
FILE | Write the records to this GenBank file. Use - for standard output. | |
--fasta_out |
FILE | Write the records to this FASTA file. Use - for standard output. | |
-e, --evalue |
NUMBER | threshold (max) E value for the domain hit. Default: no cutoff. | |
--max_overlap |
NUMBER | 1.0 | the maximum fraction of overlap between domains to be included in the annotated genbank. |
--contigs |
STRING ... | only annotate contigs with ids in this list. Additive with --contigs_file. default: annotate all contigs. | |
--contigs_file |
FILE | only annotate contigs with ids listed in this file (one per line). Additive with --contigs. default: annotate all contigs. | |
--domains |
STRING ... | Remove all domains NOT matching these names | |
--domains_file |
FILE | text file containing names of domains to include. (all domains not matching this list will be removed). | |
--keep_databases |
STRING ... | Remove annotations from all databases except these. Applied before other filters, such as domains, evalue, and max_overlap. By default will keep all annotations from all databases. | |
--databases |
STRING ... | Only filter annotations from these databases, according to evalue, domains, and max_overlap; annotations from other databases are left as they are. By default, annotations from all databases are filtered. | |
--annotation_type |
{domainator,domain_search,all} | all | Which type of annotations to filter (domainator, domain_search, all). |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.