Could not find obo file psi-ms-4.1.12

[harshhpareek]

I'm trying to read a .MZML file and I'm getting the following error:

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-5-d2ca24e06fc2> in <module>()
      1 for spectrum in msreun:
----> 2     if spectrum is not None and spectrum['ms level']==2:
      3         s = spectrum
      4         break

C:\ProgramData\Anaconda3\lib\site-packages\pymzml\spec.py in __getitem__(self, accession)
    680         else:
    681             if not accession.startswith('MS:'):
--> 682                 accession = self.calling_instance.OT[accession]['id']
    683             search_string = './/*[@accession="{0}"]'.format(accession)
    684 

C:\ProgramData\Anaconda3\lib\site-packages\pymzml\obo.py in __getitem__(self, key)
    107     def __getitem__(self, key):
    108         if not self.__obo_parsed:
--> 109             self.parseOBO()
    110 
    111         for lookup in self.lookups:

C:\ProgramData\Anaconda3\lib\site-packages\pymzml\obo.py in parseOBO(self)
    173             obo_file = obo_file + '.gz'
    174         else:
--> 175             raise IOError("Could not find obo file {0}".format(obo_file))
    176 
    177         with open(obo_file, 'rb') as fin:

OSError: Could not find obo file C:\ProgramData\Anaconda3\lib\site-packages\pymzml\obo\psi-ms-4.1.12.obo`

In the github directory and in my installation, the last one is psi-ms-4.1.12.obo. What should I do?

[MKoesters]

Hi, I just added the obo version 4.1.12 to this git. Just do a pull and everything should work. If not, just leave another comment and I'll have a closer look

Best, Manuel