CLI reference

domainator enum_report

Tabulate properties of each contig, CDS, or domain.

Writes record-wise information from Genbank files into tab-separated or html tables

Takes a genbank file which has been annotated using Domainate, write tabulated descriptions of each contig, CDS, or domain.

Give at least one of these outputs: --tsv_out, --html_out, --json_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, --tsv_out	FILE		Write the table to this tab-separated file. Use - for standard output.
--html_out	FILE		Write the table in html format to this file. Use - for standard output.
--json_out	FILE		Write streaming NDJSON (one compact JSON object per record) to this file. Use - for standard output.
--html_max_height	INTEGER		Max height in pixels to set the html output to.
--contigs	STRING ...		only examine contigs with ids in this list. Additive with --contigs_file. default: all contigs.
--contigs_file	FILE		only examine contigs with ids listed in this file (one per line). Additive with --contigs. default: all contigs.
--by	{contig,cds,domain}	contig	One line in output for every by contig, cds or domain. For protein genbanks, contig and cds are treated the same.
--partial	{include,exclude,only}	include	Which rows to report, 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. By contig, a nucleotide contig is a fragment if any of its CDSs is. By domain, the CDS or protein the domain is on decides.
--databases	STRING ...		Ignore domain annotations not from these databases. default: consider all databases.
--columns	columns...		The columns to report, in order. A column with arguments takes them after ':', as in 'qualifier:CDS:product'. Can be given more than once.
--taxonomy_update			If taxonomy database exists, check it against the version on the ncbi server and update if there is a newer version.
--ncbi_taxonomy_path	DIR	/tmp/ncbi_taxonomy_sean	Path to NCBI taxonomy database directory. Will be created and downloaded if it does not exist.
--column_names	STRING ...		If supplied, then this list will be used instead of the default column names.

Columns

Column	Description
domains	the domain names, in alphabetical order and separated by '; ', each listed once.
domain_descriptions	the domain descriptions, in alphabetical order of domain name and separated by '; ', each listed once.
score	the sum of the domain scores.
identity	the sum of the domain identities.
architecture	the domain names in order of start position, separated by '; '.
architecture_detailed	the domain architecture in order of start position. Within each CDS, domains are separated by '/'; CDSs are separated by ';'. CDSs with no domains are 'no_domains'.
start	the start coordinate of the feature.
end	the end coordinate of the feature.
strand	the strand of the feature.
length	the length of the contig, CDS or domain.
topology	the topology (usually only meaningful with --by contig).
sequence	the sequence of the contig, CDS or domain.
cds_count	the number of CDSs.
domain_count	the total number of domains.
definition	the record's definition line.
filename	the name of the input file the record came from.
domain_search	several columns describing the record's best domain_search hit: best_query, query_description, query_start, query_end, query_length, match_start, match_end, match_strand, match_score, match_identity.
taxid_lineage	the taxids from the root to the record's taxid, separated by ';'.
taxname_lineage	the taxon names from the root to the record's taxid, separated by ';'.
rank_lineage	the ranks from the root to the record's taxid, separated by ';'.
taxid:rank[:...]	the taxid at each given rank (e.g. domain, genus, species; 'self' for the record's own taxid), in columns named taxid_[rank].
taxname:rank[:...]	the taxon name at each given rank (e.g. domain, genus, species; 'self' for the record's own taxon), in columns named taxname_[rank].
qualifier:feature:qualifier	the values of this qualifier on features of this type, separated by ';'.
feature_count:feature	the number of features of this type.
motif_count:motif	the number of matches of this PROSITE motif in the sequence (nucleotide motifs for nucleotide sequences, protein motifs for proteins; see https://emboss.sourceforge.net/apps/release/6.5/emboss/apps/fuzzpro.html).
isoelectric_point	the isoelectric point of the protein. Only defined for contigs with exactly one protein (a nucleotide contig with one CDS, or a protein record).
net_charge:pH	the net charge of the protein at this pH. Only defined for contigs with exactly one protein.
repeat_count:length	the number of repeats of at least this length; for example AGGKKK has repeat_count_1 = 3, repeat_count_2 = 2 and repeat_count_3 = 1.
named_domain_count:domain	the number of Domainator domains with this name, in a column named named_domain_count_[domain].
starts_with	the first character of the sequence.
molecular_weight	the molecular weight of the sequence in Daltons, for protein, DNA or RNA according to its molecule type.
partial_count	the number of partial CDSs: by contig, the CDSs with '<' or '>' in their location (for a protein record, 1 if it is a fragment); by cds, 1 if the CDS or protein is a fragment, otherwise 0; by domain, 1 if its CDS or protein is a fragment, whether or not the domain reaches the missing end.
fragment	whether the protein or CDS is a fragment: complete, N (missing the N-terminus), C (missing the C-terminus), NC (missing both), or ? (missing ends unknown, e.g. from a UniProt ' (Fragment)' or MGnify 'FL=0' header). Only for rows that are a single protein or CDS; otherwise empty, with a warning.
append:name:type:value	a column with this name and type (str, int or float) holding this value in every row.

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