Pass energy parameter file to locarna_rnafold_pp

[mmiladi]

Hi @s-will,

What do you think of having optional parameter to pass an energy param file to locarna_rnafold_pp?
--paramFile=paramfile
I'll start implementing that, first wanted to know your opinion and be sure it is not already integrated inside locarna :)

Best,
M

[s-will]

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.

[mmiladi]

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.

[s-will]

Actually, I am using locarna_rnafold_pp in mlocarna, but for some special cases, where locarna_rnafold_pp misses the functionality, I fall back to RNAfold---I agree, this construction is a little weird (aka historically grown) ;)

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On 03/03/2017 05:16 PM, Milad Miladi wrote: 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. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#20 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALTKrQCe6LBPZ1sjmnCzkQnYjhxwi2Csks5riDzngaJpZM4MRLGl>.

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