After using ms_data = mzxml.MzXML(filename) the file stays open on Windows.

[sorenwacker]

I wonder if I have to call some method to close the file? On Linux I did not experience any trouble, but on Windows processed files cannot be deleted.

I open the file with

ms_data = mzxml.MzXML(fn)

And then iterate through the data to generate a pandas dataframe. Then the data is stored in a different format.

while True:
        try:
            data = ms_data.next()     
            df = pd.DataFrame({col: np.array(data[col]) for col in cols} )
            slices.append( df )
        except:         
            break 

How can I close the file again? I looked in the documentation, but did not find a related method.

[levitsky]

Hi! This aspect is consistent with how you work with file objects.

Accordingly, there is a .close() method on all readers. You should be able to do:

ms_data.close()

Alternatively, you can use the with syntax, e.g.:

with mzxml.MzXML(fn) as ms_data:
    for data in ms_data:
         df = pd.DataFrame({col: np.array(data[col]) for col in cols})
         slices.append( df )

This will close the file automatically.

[levitsky]

Hi @soerendip, was I able to answer your question?

[sorenwacker]

Yes, thank you. I had not seen the .close() method in the docs, but it makes total sense :-)

[levitsky]

Thanks! For reference, the .close() method is mentioned in the docs here: https://pyteomics.readthedocs.io/en/latest/data.html#general-notes.