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Rappsilber-Laboratory / xiSPEC_website

http://www.spectrumviewer.org
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PXD006574 #16

Closed colin-combe closed 6 years ago

colin-combe commented 6 years ago

both the monomer and dimer datasets in PXD006574 produce an error when uploaded to spectrumviewer.org (by specifying the PRIDE accession) 

log id: qgvv1larr1j6tdd91ga3gnjqt3_1519211636.log (include this in the github issue)
error type: Error
message: list index out of range
id: undefined

https://www.ebi.ac.uk/pride/archive/projects/PXD006574

lars-kolbowski commented 6 years ago

found the problem: the mzid uses the wrong cvTerm ''cross-link receiver' instead of "cross-link acceptor" Probably best to change to check for MS:1002510 instead of the string or what do you think?

colin-combe commented 6 years ago

yes, checking for MS:1002510 probably better

lars-kolbowski commented 6 years ago

might be a bit more difficult/time consuming. Will talk to you about it tomorrow. Put in a temp fix for now. Files are now getting parsed but it seems like there are problems with the MGF 0/1 based index... Also lot's of N-terminal cross-links in these files apparently. Their display in the FragKey could be improved I guess.

colin-combe commented 6 years ago

there are problems with the MGF 0/1 based index...

Closing this issue as we no longer suffer from this misunderstanding about MGF files