Question: Example Python code for ViennaRNA
0
gravatar for joshualevipayne
7 days ago by
Zurich
joshualevipayne70 wrote:

Hi Biostars,

I'm trying to work with the Python distribution of ViennaRNA. I've found almost no documentation, except for a few examples posted here:

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/helloworld_swig.html#helloworld_python

I can replicate these, but I'm lost trying to use functions not included in these examples. I'm particularly interested in code that compares the distance of secondary structures, for example by using RNA.make_tree() and RNA.tree_edit_distance(). Anyone have functioning Python code for this? Otherwise, anyone know where to find relevant documentation?

Thanks, Josh

ADD COMMENTlink written 7 days ago by joshualevipayne70
1

It seems that the python library is just wrapper code around the original C binaries. I can't see any python-specific documentation either really, so you are probably just going to have to do some trial and error and look at the source code for the wrapper functions.

You can inspect python objects with dir(thing) and help(thing) which might get you some of the way. You may have to refer to the documentation for the C programs to understand what the expected inputs etc are going to be I'm afraid.

ADD REPLYlink written 7 days ago by Joe18k
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