CLI reference

domainator extract_unannotated

Extract the regions of proteins not covered by any domain annotation.

Extract unannotated regions

Takes a genbank file which has been annotated using the domainator program, looks for the specified domains, and extracts regions not containing them.

This tool supports only protein sequences.

can write a fasta or a 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 filenames. 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.
--include_taxids	INTEGER ...		Include these NCBI taxids and their descendants (OR).
--exclude_taxids	INTEGER ...		Exclude these NCBI taxids and their descendants; exclusions take precedence.
--taxonomy_expr	STRING		Boolean expression over taxid lineages using &, |, ~, and parentheses, e.g. "2 & ~1224". Mutually exclusive with include/exclude_taxids.
--taxonomy_unknown	{exclude,include,evaluate,error}	exclude	Unresolved taxonomy: exclude (default), include, evaluate against an empty lineage, or error. With ~2, exclude rejects unlabeled candidates; evaluate and include allow them. Only active with taxonomy criteria. Not inverted.
--ncbi_taxonomy_path	DIR	/tmp/ncbi_taxonomy_sean	NCBI taxonomy database directory; downloaded if missing and filtering is active.
--taxonomy_update			Check for an updated taxonomy database when filtering is active.
--contigs	STRING ...		Only read input protein records with these IDs; restricts where extraction occurs. Additive with --contigs_file; duplicate names are ignored. If neither source is supplied, no name criterion is applied.
--contigs_file	FILE		Only read input protein records with these IDs; restricts where extraction occurs. Read names from a plain-text file (one per line), FASTA/GenBank record IDs, or HMM profile names. Additive with --contigs; duplicate names are ignored. Plain-text lines are stripped and blank lines ignored. An empty file adds no names; if no names are supplied directly either, the resulting list is explicitly empty, not an omitted criterion.
-e, --evalue	NUMBER		Count only domain/search-hit annotations with e-value <= this when finding unannotated gaps. Default: no cutoff.
--min_annotation_score	NUMBER		Count only domain/search-hit annotations with score >= this when finding unannotated gaps. Raising this can enlarge the gaps. Default: no cutoff.
--databases	STRING ...		Only consider domains from these databases. default: all databases.
--annotation_type	{domainator,domain_search,all}	domainator	Which annotations count as annotated. domainator: domain annotations (from domainate). domain_search: best-hit annotations (from domain_search). all: both.
--keep_direction			Has no effect: this tool supports only protein sequences and never reverse-complements them. Retained for compatibility with extract_domains.
--keep_parent_id			Use the parent protein ID instead of a coordinate-based region ID. This can produce duplicate IDs for different extracted sequences.
--largest			Extract only the largest unannotated region from each protein, providing it passes the length cutoff specified by --min_region_length
--min_region_length	INTEGER		Extract only unannotated gaps of at least this many amino acids, before choosing --largest. Not a cutoff on the input protein length. Default: no cutoff.

Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.