Bug in mapdamagegeomparam script: AttributeError: 'DataFrame' object has no attribute 'ix'

[jfy133]

Bug

I was trying out tapas and came across the following bug, when running the following I would get the error:

❯ $TAPAS/mapdamagegeomparam --fit-plots fig/fit.png input/mapdamage/misincorporation.txt
Traceback (most recent call last):
  File "/raven/u/jfellowsy/bin/tapas-1.2/scripts/src/mapdamage2geomparam.py", line 436, in <module>
    if __name__=="__main__": main()
  File "/raven/u/jfellowsy/bin/tapas-1.2/scripts/src/mapdamage2geomparam.py", line 68, in main
    A = A.ix[A.Total != 0,:]
  File "/u/jfellowsy/conda-envs/tapas/lib/python3.9/site-packages/pandas/core/generic.py", line 5465, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

This is derived from this line:

tapas/scripts/src/mapdamage2geomparam.py

Line 68 in 6d7e273

A = A.ix[A.Total != 0,:]

Where the ix column doesn't exist in the input mapDamage2 misincorporation file.

Workaround

Delete the referred to line in the above script, that refers to ix (assuming your misincorporation file doesn't have any 0s).

I was then successfully able to get the script ot run prpoerly.

[mlell]

Hi,
on new versions of the pandas package DataFrame.ix seems to have been replaced by .loc. Thanks for this, I'll look into it
https://stackoverflow.com/questions/59991397/attributeerror-dataframe-object-has-no-attribute-ix

[jfy133]

Ah that could be the issue. I tried to install all the dependencies with exact versions via bioconda (for reproducibility) but unfortuanately I couldn't this to work due to conflicts or versions that are too old for bioconda.

I've therefore 'blindly' installed the latest versions of everything and somewhat hoping for the best.

conda create -n tapas -c bioconda python=3 r-essentials=4.0 r-base=4.0.3 bwa=0.7.17 bowtie2=2.4.2 minimap2=2.18 hisat2=2.2.1

Could be the pandas version I installed therefore wasn't compatible.