domainator sort_contigs
Sort contigs by their Domain_Search score.
Sort contigs by Domain_Search score.
This matches the output ordering used by domainator domain_search when --max_hits is set.
It is primarily intended for post-processing domain_search output written without
--max_hits, where the temporary hit_best_score annotation is not preserved in the
written GenBank file.
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 | GenBank files. 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. | |
--max_hits |
INTEGER | Maximum number of contigs to return, keeping the best-scoring ones. If not supplied, return all contigs. | |
--domains |
STRING ... | If supplied, sort by the best Domainator annotation score from domains with these names instead of Domain_Search annotation scores. Additive with --domains_file. | |
--domains_file |
FILE | Like --domains, but read the domain names from this file, one per line. Additive with --domains. | |
--databases |
STRING ... | When used with --domains, only consider Domainator annotations from these databases. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.