CLI reference

domainator build_ssn

Build a sequence similarity network for Cytoscape or the Domainator Viewer.

Generates Sequence Similarity Networks

Build a sequence similarity network and do analysis related to that: write it for Cytoscape
(--xgmml_out) or for the Domainator Viewer (--html_out, --dvb_out).

Give at least one of these outputs: --xgmml_out, --html_out, --dvb_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	pairwise similarity (or distance) scores. In the network, nodes will be derived from row and column names, and edges will be added between pairs of rows and columns meeting the threshold criteria. Format can be tab-separated text, or Domainator hdf5.
--threshold	NUMBER	0	keep only edges with weights strictly above this value. This should be >= 0.
--metadata	FILE ...		tab separated files of sequence metadata.
--subset	STRING ...		Only consider matrix labels in this list. Additive with --subset_file.
--subset_file	FILE		text file containing matrix labels to retain.
--color_by	STRING		Color the points in the output image based on this column of the metadata table.
--color_table	FILE		tab separated file with two columns and no header, columns are: annotation, hex color. For example: CCDB cc0000
--max_color_groups	INTEGER		Give distinct colors only to this many of the largest --color_by groups, all remaining groups share a neutral gray. By default every group gets a color, cycling over a palette of 64 distinguishable colors.
--palette_offset	INTEGER	0	Skip this many colors at the start of the palette before assigning colors to --color_by groups. For example, if a network colored by one column used the first 5 colors, --palette_offset 5 colors another column without reusing them. Ignored with --color_table.
--mark_mst			Give every edge a boolean 'MST' property saying whether it belongs to the maximum spanning tree. Useful for styling or filtering the MST backbone within a larger network in Cytoscape.
--color_table_out	FILE		tab separated file with two columns and no header, columns are: annotation, hex color. Written after the color table is updated with new colors, for example if using --color_by, but not supplying an external color table.
-o, --xgmml_out	FILE		Write the network to this Cytoscape xgmml file.
--html_out	FILE		Write the Domainator Viewer, showing this network, to this HTML file. The viewer shows the network's maximum spanning tree above --threshold, whatever --mst and --knn say.
--dvb_out	FILE		Write the gzip-compressed JSON Domainator Viewer bundle (.dvb) to this file. The viewer opens it (domainator viewer), and saves sessions in the same format.
--merge_impact_metric	{product,min_child}	min_child	How the viewer's split chart measures a merge: min_child (node count of the smaller piece) or product (the two piece sizes multiplied). Switchable in the viewer.
--label_by	STRING		Label the nodes in the html viewer by this metadata column at first.
--categorical	STRING ...		Numeric metadata columns (for example integer cluster numbers) that the html viewer should color as discrete categories instead of a gradient.
--name	STRING		The network's name, shown in the html viewer. Defaults to the html (or dvb) output's file name.
--cluster			Creates a new metadata column called 'SSN_cluster', replacing that column from the metadata file if already present. Finds clusters by following connectivity, assigns each cluster a distinct integer, based on size rank, bigger clusters get smaller numbers.
--cluster_tsv_out	FILE		Path to write a tsv file mapping each sequence to its cluster. If set, then --cluster is automatically activated. If --no_cluster_header is not set, then the file will have the header: contig cluster.
--no_cluster_header			If set, then the tsv file will not have a header. Only relevant if --cluster_tsv_out is set.
--max_output_gb	NUMBER	25.0	Fail if a projected output file would exceed this many GB. Set to 0 to disable the guardrail.
--mst			Keep only the edges of the maximum spanning tree (forest). The clusters (connected components) are the same as the full graph's, with the connections inside each cluster pruned to the minimum needed to keep it connected. Combine with --knn to also keep each node's nearest neighbors.
--knn	INTEGER		Keep only OR-symmetric K-nearest-neighbor edges (K >= 1): an edge is kept if it is among the K best for either of its nodes. On its own this can split a cluster of the full graph into several; add --mst to keep the clusters connected.

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