pymzML "psi-ms.obo" file issue

[Zhixu Ni]

Dear LipidHunter users,

We just observed some common issue that Step I is not functioning.

Some of the error is due to the pymzML package that LipidHunter used to read mzML files.

In some cases, the pymzML package cannot find the "psi-ms.obo" file under the \pymzml\obo folder, and will report an error.

##For source code version users ##

Please find the obo.py file in the pymzML package folder, and edit this section (in my version from line 145 to 149)

        obo_file = os.path.join(
            obo_root,
            'obo',
            "psi-ms{0}.obo".format('-' + self.version if self.version else '')
        )

And change to

        obo_file = os.path.join(
            obo_root,
            'obo',
            "psi-ms.obo"
        )

And make sure that you have the psi-ms.obo file under pymzml\obo folder. If you cannot find a file named exactly as psi-ms.obo but many other .obo files, please copy the latest version of the .obo file e.g. psi-ms-3.79.0.obo to psi-ms.obo.

I hope this will solve your issues.

##For windows .exe version users. ## Currently we did not observed this problem on our computers, since the obo files were packed with LipidHunter and pymzML usually can find them. If you meet any problems, please do not hesitate to post an issue here, we will have a look as soon as possible.

Thanks for choosing LipidHunter for your lipid identification.

Zhixu Ni