plotCoverage.py error: Values instance has no attribute 'working_Dirpath'

Question

[mthm]

I am trying to run plotCoverage on the TE consensus library and the gff file of coordinates to visualize the results:

plotCoverage.py -i XXX_refTEs.gff -f gff3 -q XXX_refTEs.fa --merge -l grey -o plotCoverage

the error is:

Traceback (most recent call last):
  File "/usr/local/SMART/Java/Python/plotCoverage.py", line 464, in <module>
    pp.setOutput(options.outputFileName if os.path.isabs(options.outputFileName) else os.path.join(options.working_Dirpath, options.outputFileName))
AttributeError: Values instance has no attribute 'working_Dirpath'
Exception AttributeError: "'PlotParser' object has no attribute 'outputFileName'" in <bound method PlotParser.__del__ of <__main__.PlotParser object at 0x7f5368a78410>> ignored

the versions are:

Plot Coverage v1.0.1
matplotlib: 2.2.3

anybody has any idea of why this happens?

Answer 1

[mthm]

as always, I am answering my own question, how weird is that!! I should have provided the absolute path to the plotCoverage directory after the -o, or probably using the -D flag would work as well.

[Ram]

as always, I am answering my own question, how weird is that!!

You're the person most invested in solving your problems, so it's not really weird. Plus, you could be working on stuff that very few people here work on (or the problems you're facing are pretty specific to your environment), so not many users can help you out before you find an answer yourself.

In any case, you're doing a great job following up on your posts - and that is great for all other forum users (including future you). Thank you for that!