isBigWig segfault about pybigwig

[dpryan79]

I'm not surprised, you're calling object methods directly and giving them numbers instead of an appropriate object. The appropriate syntax is:

import pyBigWig
bw = pyBigWig.open("test.bw")
bw.isBigWig() # or bw.isBigBed()

pyBigWig.pyBigWig doesn't exist, so it can't be exported.

[clemenshug]

I see, I wasn't aware that these are strictly object methods since they are available as functions on the module level.

What I want do to do is simply checking if a variable is a pyBigWig object instance. So far I've used isinstance(var, pyBigWig.pyBigWig). I'm not so sure now if this was intended, but in Python 3 pyBigWig.pyBigWig does point to the pyBigWig.bigWigFile type, so this works nicely.

What would be the suggested way to test this? I guess I could do hasattr(var, 'isBigWig') for now. Thank you for your help!

[dpryan79]

I guess I could remove them from the module, it was easier to just leave them in since then the documentation is easier and I didn't have to figure out how else it's all supposed to work in the python C API.

Regarding testing whether an object is a bigWig file, i've never had reason to do that and thus never implemented anything. The bigWigFile is the object that's actually returned by open(), so perhaps checking that with isinstance() works. If not, I can look into implementing something.

[dpryan79]

Ah, I found how to fix the documentation so the object methods aren't listed being directly accessible. I also found where I forgot to add the pyBigWig object to the module. I'll try to get a new version released with all of that fixed in the next week.

[dpryan79]

I've just pushed out a new version, where the documentation for this is fixed.