Unparseable number during XiFDR

[aaprap]

Heya,

I ran .d-data (Q-TOF) through xiSearch (v2.1.5.5), which exported an CSV-file to the results-folder without any issues. Hereafter, I tried to run it through xiFDR (v1.7.6.7) for validation, and the first error that occurred was:

Jan 06, 2023 14:32:18 PM org.rappsilber.data.csv.CsvParser setCurrentLine
WARNING: line 2 contains more fields than ever observed!

I changed the text to columns in the CSV-file (columns separated by commas) through Excel, and tried to run it in xiFDR once again. Now I've got the following message, which I can't decipher:

Jan 06, 2023 14:34:37 PM org.rappsilber.fdr.CSVinFDR readCSV
SEVERE: Unexecpted exception while parsing line 1
java.lang.NumberFormatException: Unparseable number: "VFGKE"
    at org.rappsilber.data.csv.CsvParser.getInteger(CsvParser.java:930)
    at org.rappsilber.fdr.CSVinFDR.readCSV(CSVinFDR.java:288)
    at org.ruappsilber.fdr.XiCSVinFDR.readCSV(XiCSVinFDR.java:634)
    at org.rappsilber.fdr.gui.FDRGUI.addCSV(FDRGUI.java:970)
    at org.rappsilber.fdr.gui.FDRGUI.innerBatchReadCSV(FDRGUI.java:851)
    at org.rappsilber.fdr.gui.FDRGUI$10.run(FDRGUI.java:900)
    at java.lang.Thread.run(Unknown Source)

Jan 06, 2023 14:34:37 PM org.rappsilber.fdr.gui.FDRGUI$10 run
SEVERE: null
java.lang.NullPointerException
    at org.rappsilber.fdr.gui.FDRGUI.setFdr(FDRGUI.java:481)
    at org.rappsilber.fdr.gui.FDRGUI$10.run(FDRGUI.java:900)
    at java.lang.Thread.run(Unknown Source)

May I have set the CSV-file or xiFDR up wrong, or could it be something else?

I really hit a wall here, so any help or any tips are highly appreciated.

[lars-kolbowski]

Can you provide the csv file that failed? It looks like some formatting error occurred.

[lutzfischer]

could you also send the file as it was before you saved it in excel?

[lutzfischer]

I think I found the problem. The input files contain commas - and source column is not quoted correctly. So need to add quotes there. But if you could change the input file names before search to something without a comma that should work.

[aaprap]

It really just seems like, it were the commas that disrupted the parsing - Thank you for your time and help!

[lutzfischer]

Next version will quote the fields that where the problem.