README example throws error

[EthanHolleman]

Summary

Hi y'all, currently trying to get DrTransformer up and running but using the example code from the README and the fasta files from examples/ is throwing TypeError: in method 'varArrayShort___getitem__'

Programming environment

• Ubuntu 22.04 LTS
• DrTransformer installed into fresh conda env using the command provided by the README
• # INFO - DrTransformer-v1.0: RNA folding kinetics during transcription.

Shell commands and complete error message

Running cat ABCD.fa | DrTransformer --name ABCD gives the error message below. ABCD.fa is taken from the examples folder.

  11    1 ...........   0.00  [1.0000 -> 1.0000] ID = 0
Traceback (most recent call last):
  File "/home/ethollem/anaconda3/envs/drTrans/bin/DrTransformer", line 10, in <module>
    sys.exit(main())
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/drtransformer.py", line 419, in main
    nn, on, prep = TL.expand(args.profile)
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/landscape.py", line 268, in expand
    ndata, edata = neighborhood_flooding((fseq, md, fpwm), ndata, gedges, tedges = edata, minh = minh)
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/rnafolding.py", line 789, in neighborhood_flooding
    for (ss2, en2, ssB, enB, ss1, en1) in edge_flooding(fp, s2, s1, 
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/rnafolding.py", line 701, in edge_flooding
    path, barrier = findpath_split(seq, s1, s2, md, fpwm = fpwm)
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/rnafolding.py", line 562, in findpath_split
    common_basepairs(pt1, pt2)):
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/drtransformer/rnafolding.py", line 486, in common_basepairs
    return iter((i, j1) for i, (j1, j2) in enumerate(zip(pt1[1:], pt2[1:]), 1) 
  File "/home/ethollem/anaconda3/envs/drTrans/lib/python3.10/site-packages/RNA/RNA.py", line 1713, in __getitem__
    return _RNA.varArrayShort___getitem__(self, i)
TypeError: in method 'varArrayShort___getitem__', argument 2 of type 'int'

This same error is also thrown for my own RNA sequences.

Kind of scratching my head at this one, happy to provide additional info if it would be helpful. Thanks and have a good one!

[bad-ants-fleet]

Hi Ethan,

I get the same error when using the latest ViennaRNA package version. Do you use the conda installation? If so, everything should work if you rollback to:

conda install 'viennarna==2.5.1'

I'll have to check with @RaumZeit what the problem is. This may take a few weeks though.

[EthanHolleman]

Sounds good, I'll roll back ViennaRNA and report back!

Update: @bad-ants-fleet your suggestion seems to have worked perfectly. Rolled back to 2.5.1 and same commands on same input fasta ran without issue. Seems like the most recent ViennaRNA breaks something in Dr. T ...

Here is my conda environment yml file for reference exported with the --from-history and some grepping to remove all the extra nonsense conda adds to these.

name: drTransformer
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - drtransformer
  - viennarna==2.5.1

Maybe add a note to the README in the meantime :)

[RaumZeit]

Hi @bad-ants-fleet @EthanHolleman,

when I read this bug report I already had a vague idea on what might be going wrong here and today I found some time to dig into this issue a little further. So, basically, what has changed with v2.6 of the ViennaRNA Package is the handling of the ptable data structure in the Python interface. Before, those were always actual Python lists with copies of the underlying C data. Since v2.6 the data types only shadow the underlying C data structure but still behave like lists. This has the advantage that no data needs to be converted and copied over and over when underlying C functions are called from within Python.
Unfortunately, I only implemented the __getitem__ and __setitem__ methods, and thought that the remaining functionality of list-like behavior would be handled by Python. But it seems that we also need to explicitly handle slice objects to actually support slicing the ptable.
I started implementing this extension but it might take another week or two until this is finished and compatibility with v2.6 is restored. I'm on vacation right now but will be back next week...

Sorry for the inconveniences!
Best,
Ronny

[RaumZeit]

This should be fixed with v2.6.4 of the ViennaRNA Package...