Resolve conflict of CRH hidden options that are in Gene3D docs

UCLOrengoGroup / cath-tools

Protein structure comparison tools such as SSAP and SNAP

http://cath-tools.readthedocs.io

GNU General Public License v3.0

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Resolve conflict of CRH hidden options that are in Gene3D docs #44

Closed tonyelewis closed 6 years ago

tonyelewis commented 6 years ago

The Gene3D docs in gene3d_hmmsearch/README_scan.txt of ftp://orengoftp.biochem.ucl.ac.uk/gene3d/CURRENT_RELEASE/gene3d_hmmsearch.tar.gz now include a CRH command line:

./cath-resolve-hits --min-dc-hmm-coverage=80 --output-hmmsearch-aln --input-format  hmmsearch_out seqs.hmmsearch > seqs.crh

...which includes currently hidden / non-public CRH options. Does this mean that the following now need to be made public?

--min-dc-hmm-coverage
--min-hmm-coverage
--output-hmmer-aln

tonyelewis commented 6 years ago

We've discussed this a bit more and our plan is as follows.

Short term:

Leave the options hidden for now.
Internally mark-up the hidden options that are used in the Gene3D command as such so that we can remember to notify known users of any changes.

Longer term:

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 use this to improve the way the --min-dc-hmm-coverage option currently works (identifying those domains with a regular expression on the ID).
After any such changes, consider making the --min-hmm-coverage and/or any discontinuous options public.