Tool: cath resolve hits - UCLOrengoGroup/cath-tools GitHub Wiki

Notes on Possible Future Features

• Add support for parsing hmmsearch's alignment output (-A <f>: save multiple alignment of all hits to file <s>).
• Add support for parsing results from other formats (eg Blast Tabular, as also used by MMseqs2).
• Do more of the processing of discontinuous models, currently done by Gene3D (see #44).
• Consider making --output-hmmer-aln a public option.
• Make CRH handle more of the processing of discontinuous models that's currently handled by Gene3D and then:
  • Use this to improve the way the --min-dc-hmm-coverage option works (currently identifies those domains with a regular expression on the ID).
  • Consider making --min-hmm-coverage and/or any discontinuous options public.
• Improve helpfulness on failure to parse input (eg "Unable to parse/process resolve-hits input data") - eg remind the user of the possible --input-format options? Can it make some sensible attempt to guess the format? Are the hmmsearch/hmmscan inputs distinguishable?