CLI reference

domainator extract_peptides

Extract translated CDSs as protein records, keeping their domain annotations.

Converts annotated CDSs into annotated protein sequences

Takes a domainator-annotated genbank file 
Creates peptide genbank or fasta files with the domainator annotations from the CDSs found in the original
genbank file

By default, extracts peptides from all CDSs in the genbank file.

If any criteria are supplied, then only peptides from CDSs that meet the criteria will be extracted.

CDS names, domain names, domain expressions, unannotated, and search-hit presence
are OR selectors. With no selectors, all eligible CDSs are selected.
Contig IDs, strand, fragment status, and taxonomy are independent AND restrictions.
Invert negates only the combined selectors, never these restrictions. With no
selectors, invert warns and is ignored.

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 records with these IDs; not inverted by --invert. Additive with --contigs_file; duplicate names are ignored. If neither source is supplied, no name criterion is applied.
--contigs_file	FILE		Only read input records with these IDs; not inverted by --invert. 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.
--domains	STRING ...		Select CDSs containing these domain names, OR with other CDS selectors. Additive with --domains_file; duplicate names are ignored. If neither source is supplied, no name criterion is applied.
--domains_file	FILE		Select CDSs containing these domain names, OR with other CDS selectors. Read names from a plain-text file (one per line), FASTA/GenBank record IDs, or HMM profile names. Additive with --domains; 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.
--domain_expr	STRING		Boolean domain expression using &, |, ~, and parentheses. Additive with other CDS selectors.
--databases	STRING ...		Consider only domains from these databases when filtering by domain. default: all databases.
--unannotated			extract peptides from CDSs with no domain annotations.
--annotation_type	{domainator,domain_search,all}	domainator	Which annotations to select peptides by. domainator: domain annotations (from domainate). domain_search: best-hit annotations (from domain_search). all: both.
--has_search_hit			Also select existing domain_search hits, regardless of annotation_type, domain names, domain expressions, or databases. Hits must pass the e-value and score cutoffs where applicable. Participates in --invert where available.
--strand	{f,r}		Only extract peptides from CDSs on the specified strand.
--partial	{include,exclude,only}	include	Which CDSs to extract peptides from, by fragment status. include: all. exclude: skip fragments. only: only fragments. A CDS is a fragment if its location has '<' or '>', or it has a /partial qualifier. A protein record is a fragment if it has a UniProt ' (Fragment)' or MGnify 'FL=0' header, a 'Flags: Fragment' definition or NON_TER features (UniProt text entries), or a CDS/Protein feature with '<' or '>' spanning it. Not affected by --invert.
--invert			Invert the combined CDS selectors, not contigs, strand, partial, or taxonomy. With no selectors, warn and ignore.
--cds	STRING ...		only look for peptides on cdss with these names
--cds_file	FILE		only look for peptides on cdss with names listed in this text file.
--keep_parent_id			Use the original contig ID instead of the resolved CDS name for peptide IDs. This can produce duplicate IDs.
--name_field	STRING		The CDS qualifier to prefer for CDS name matching and peptide IDs. If not supplied, then qualifiers will be checked in order of: ["protein_id", "gene_id", "locus_tag", "gene"]
-e, --evalue	NUMBER		Maximum e-value of domain/search-hit annotations used for CDS selection and carried onto peptide records. Default: no cutoff.

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