beliveau-lab/OligoMiner

structureCheck.py not working for RNA

Closed this issue · 2 comments

stephenwilliams22 commented

I'm trying to evaluate secondary structor of RNA sequences with rna1995 (as defined in the NUPACK user guide http://www.nupack.org/downloads/serve_public_file/nupack_user_guide_3.1.pdf?type=pdf).

python structureCheck.py -f my.bed -F 13 -s 780 -T 50 -R -m rna1995

However, I'm getting the error

Traceback (most recent call last):
  File "/mnt/home/stephen.williams/Apps/OligoMiner/structureCheck.py", line 552, in <module>
    main()
  File "/mnt/home/stephen.williams/Apps/OligoMiner/structureCheck.py", line 544, in main
    startTime,
  File "/mnt/home/stephen.williams/Apps/OligoMiner/structureCheck.py", line 384, in runStructureChecker
    sc.run()
  File "/mnt/home/stephen.williams/Apps/OligoMiner/structureCheck.py", line 154, in run
    p = self.prob_check(probeSeq, struct_in)
  File "/mnt/home/stephen.williams/Apps/OligoMiner/structureCheck.py", line 124, in prob_check
    prob_val = float(p.stdout.readlines()[14])
ValueError: could not convert string to float: % Magnesium concentration: 0.0000 M

I assume structureCheck.py is trying to convert -m rna1995 to a float.

Thanks for your advice on how to move forward.

conorcamplisson commented

Thanks for bringing this to our attention. It looks like the cause of this issue was that NUPACK adds this warning message to its output when run in RNA mode:

% ************************************************************************  %
% WARNING: No salt corrections availabe for RNA.  Using 1 M Na and 0 M Mg.  %
% ************************************************************************  %

and so the resulting prob value was not on the line of stdout where the python code was expecting to find it.

I've updated the stdout parsing logic so that it finds the prob value and also alerts the user to this caveat about salt corrections being ignored in RNA mode.

Let me know if you run into any other issues!