Usage: cath-map-clusters [options] <input_file>
Map names from previous clusters to new clusters based on (the overlaps between)
their members (which may be specified as regions within a parent sequence).
Renumber any clusters with no equivalents.
When <input_file> is -, the input is read from standard input.
-h [ --help ] Output help message
-v [ --version ] Output version information
--map-from-clustmemb-file <file> Map numbers from previous clusters specified in <file> to their equivalents in the working clusters where possible and
if all the cluster names in <file> are positive integers, renumber leftover new clusters from one plus the largest
or if not, rename with new_cmc_cluster_1, new_cmc_cluster_2, ...
(of, if unspecified, renumber all working clusters from 1 upwards)
--read-batches-from-input Read batches of work from the input file with lines of format: `batch_id working_clust_memb_file prev_clust_memb_file` where:
* batch_id is a unique label for the batch (with no whitespace)
* prev_clust_memb_file is optional
--min_equiv_dom_ol <percent> (=60) Define domain equivalence as: sharing more than <percent>% of residues (over the longest domain)
(where <percent> must be â¥ 50)
--min_equiv_clust_ol <percent> (=60) Define cluster equivalence as: more than <percent>% of the map-from cluster's members having equivalents in the working cluster
[and them being equivalent to > 20% of the working cluster's entries and > 50% of those that have an equivalence]
(where <percent> must be â¥ 50%)
--append-batch-id <id> Append batch ID <id> as an extra column in the results output (equivalent to the first column in a --multi-batch-file input file)
--output-to-file <file> Write output to file <file> (or, if unspecified, to stdout)
--summarise-to-file <file> Print a summary of the renumbering to file <file>
--print-entry-results Output the entry (domain)-level mapping results
--sorting-help Show the criteria for sorting unmapped clusters
The input cluster-membership data should contain lines like:
...where domain_id is a sequence/protein name, optionally suffixed with the domain's segments in notation like '/100-199,350-399'. The suffixes should be present for all of the domain IDs or for none of them. Domains shouldn't overlap with others in the same cluster-membership data.
Input data doesn't have to be grouped by cluster.
NOTE: When mapping (ie using --map-from-clustmemb-file), the mapping algorithm treats the two cluster membership files differently - see --min_equiv_clust_ol description.
Please tell us your cath-tools bugs/suggestions : https://github.com/UCLOrengoGroup/cath-tools/issues/new