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Rappsilber-Laboratory / build-xiview

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Import of XiFDR.csv data in XiVIEW #68

Closed wendscheck closed 4 years ago

wendscheck commented 4 years ago

Hi, like to import my >filename<Xi1.7.0_PSM_xiFDR1.4.1.csv in XiVIEW, but have several issues with that. I'm choosing this table, cause i have to do some python-based filtering between export from XiFDR and import in XiVIEW. My data looks exactly like the example csv data (PolII_XiVersion1.6.742_PSM_xiFDR1.1.27.csv downloaded from https://xiview.org/xiNET_website/upload.php) and during the upload i get no warnings or errors. But, i have a set of links which should be displayed as homomultimeric links, but they are not and are displayed as intra-links instead. I recognized that for those links i have two semicolon separated values in the column 'PepPos' (displayed by XiView after click on the link), which makes no sense to me and could be one reason for this issue. When i look up the column 'PepPos1' and 'PepPos2' in my csv manually i can't find any abnormal features. Do you have any idea how to fix this?

colin-combe commented 4 years ago

i have a set of links which should be displayed as homomultimeric links, but they are not and are displayed as intra-links instead. I recognized that for those links i have two semicolon separated values in the column 'PepPos' (displayed by XiView after click on the link), which makes no sense to me and could be one reason for this issue.

Yes, I think you have correctly intuited the reason.

The semicolon seperated values in the PepPos columns indicate that the position of the peptide is ambiguous, that the peptide occurs in more than one location in your search sequences. (Each semicolon separated value is a different possible position.)

If these peptides do not occur in more than one place and are being incorrectly marked as ambiguous then something has gone wrong and please let us know.

cheers, colin

colin-combe commented 4 years ago

it was like you thought.

there was a bug introducing the two values with a semi-colon between them

i think it should be fixed now, let me know if not

the bug was in the parser on the server side, not the javascript that runs in the browser, so you will have to upload your data again for it to be fixed