Comments (3)
Alignment with different parameter files is currently supported only by mlocarna (--rnafold-parameter).
Currently, mlocarna does call RNAfold instead of locarna_rnafold_pp, if this option is given.
Of course, it would be interesting to migrate this feature into the Locarna lib and rnafold_pp, since then we could use this even for calls to locarna/locarna_p/sparse (without the need for mlocarna).
btw, there are also some other features of RNAfold that would be cool to have :).
If you want to add paramFile (and maybe other such features), the additional parameters should be passed to RnaEnsemble via PFoldParams. In RnaEnsembleImpl, the two folding methods (regular and alifold) that generate the McCaskill matrices should be extended: compute_McCaskill_matrices and compute_McCaskill_alifold_matrices. For SPARSE, one also must make sure that extensions do not break the inloop probs computation.
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Thanks much for the detailed info. I thought you use locarna_rnafold_pp inside mlocarna. We wanted to check it for the Bralibase benchmarking, so for the moment --rnafold-parameter was fine.
However I would be happy to contribute and extend locarna_rnafold_pp, maybe we could think of useful options that could be added there and I start working on it.
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Related Issues (20)
- handling of empty input sequences HOT 1
- Passing --LP gives the error: only one of the options --noLP and --LP can be defined at a time. HOT 1
- spurious output
- control size of output directory
- empty names in input
- provide distances in tree
- error: implicit instantiation of undefined template HOT 2
- No rule to make target 'exparna_p.1', needed by 'all-am'. Stop. HOT 1
- 2.0.0-RC8 fails: No rule to make target 'exparna_p.1' HOT 4
- "Can not read alignment file results/result.aln" in refinement of alignment HOT 1
- running local - two files. HOT 3
- 'make check' fails at locarnate 'Calculate multiple alignment...' HOT 1
- no structure annotation in stockholm file with 2.0.0RC8 HOT 1
- mlocarna realign of stk input
- 'make check' fails HOT 2
- locarna --probabilistic fails to read arc scores HOT 2
- Cannot compute match probabilities
- No colors in mLocARNA structure predictions from conda installation HOT 3
- mlocarna stumbles over `--width` HOT 3
- alingment ID in STOCKHOLMs output HOT 2
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