parseMSA

[estrauch]

somehow parseMSA will not work, even if fetched from PFAM.
the MSAFile object does work, though. Any suggestions?

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RuntimeError Traceback (most recent call last)
RuntimeError: module compiled against API version 0x10 but this version of numpy is 0xe

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ImportError Traceback (most recent call last)
Input In [27], in <cell line: 1>()
----> 1 parseMSA('PF02171_full.sth')

File ~/anaconda3/lib/python3.9/site-packages/prody/sequence/msafile.py:591, in parseMSA(filename, **kwargs)
589 msaarr = empty(filesize, '|S1')
590 elif format == SELEX or format == STOCKHOLM:
--> 591 from .msaio import parseSelex as parser
592 msaarr = empty(filesize, '|S1')
593 elif format == CLUSTAL:

ImportError: numpy.core.multiarray failed to import

[jamesmkrieger]

You probably need to build your prody c extensions again because your numpy doesn’t match.

If you have installed prody as a normal pip install from PyPI then you probably want to uninstall it and install it again.

If you have a development installation from source then you should run this again:
python setup.py build_ext —inplace —force

Let us know if that works

[estrauch]

thanks for the quick reply. I uninstall with pip and install package with build and install using the source code download. Now it is working! Thanks!

[jamesmkrieger]

great!