A simple way to map between different partitions (clusterings, sub-groupings) of a group of entities. Accounts for equivalences between domains specified on slightly differing regions of a parent sequence. Renumbers any clusters with no equivalents.
The current full
--help usage information is:
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. Miscellaneous: -h [ --help ] Output help message -v [ --version ] Output version information Input: --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 Mapping: --min_equiv_dom_ol <percent> (=60) Define domain equivalence as: sharing more than <percent>% of residues (over the longest domain) (where <percent> must be ≥ 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 ≥ 50%) Output: --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 Detailed help: --sorting-help Show the criteria for sorting unmapped clusters The input cluster-membership data should contain lines like: cluster_name domain_id ...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
Sorting criteria for new, unmapped clusters
- Descending on sum over domains of
sqrt(total_dom_length)(ie clusters with more/longer sequences come earlier, with more emphasis on having more sequences)
- Descending on number of sequences (ie clusters with more sequences come first)
- Ascending on average mid-point index (ie clusters with domains earlier in their sequences come first)
- Ascending on first domain ID
If neither of a pair of clusters is preferred by one criterion, the comparison drops down to the next.
Please tell us about your cath-tools bugs/suggestions here.