Tool to split merged result files from pFind

[Hsin Tang]

Hello, I am interested in using PANDA to analyze pFind results. The readme describes a tool to split pFind results where all raw files were searched together. I am wondering if the tool is already available? Thank you!

[BPRC-Bioinformatics]

Hi, sorry for the late reply. The split tool is already done but recently I have to work at home due to the pandemics. So I plan to take some extra time to rewrite the code and upload to SourceForge by the end of this month. Thank you for using PANDA and PANDA-view.

[Hsin Tang]

Thank you. Eagerly looking forward to it. Stay safe.

[BPRC-Bioinformatics]

Hi, I just upload the split tool for pFind3 and pGlyco2, you can find it in the PANDA website or in the attachment. The pFindSplit tool only runs in CMD. The command is easy: pFindSplit.exe c:\test\test.protein or test.filtered.spectra.

[Hsin Tang]

Thank you! I will test it out and let you know if I encounter any problem.

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From: BPRC-Bioinformatics carlos-chang@users.sourceforge.net
Sent: Monday, May 11, 2020 11:41 PM
To: [panda-tools:discussion] general@discussion.panda-tools.p.re.sourceforge.net
Subject: [panda-tools:discussion] Tool to split merged result files from pFind

Hi, I just upload the split tool for pFind3 and pGlyco2, you can find it in the PANDA website or in the attachment. The pFindSplit tool only runs in CMD. The command is easy: pFindSplit.exe c:\test\test.protein or test.filtered.spectra.

Attachments:

• pFindSplit_release20200512.ziphttps://sourceforge.net/p/panda-tools/discussion/general/thread/e221542c62/8580/attachment/pFindSplit_release20200512.zip (24.6 kB; application/x-zip-compressed)

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Tool to split merged result files from pFindhttps://sourceforge.net/p/panda-tools/discussion/general/thread/e221542c62/?limit=25#8580

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[Hsin Tang]

Hi,

I tried the split tool, but unfortunately it did not work for me. Below is the error:

W:\pFind\Data\EischenC\20-L014\Combined\result>pFindSplit.exe pFind.protein
Loading the protein file from pFind results: pFind.protein
Cannot find the right folder path from the input file!
0 files are split from the input filethe total time of pFindSplit is 0.00s.

Any help is appreciated.

Thanks.

[BPRC-Bioinformatics]

Hi,

Thank you so much for the feedback:)
It was because I assumed the users should use the absolute path of the input file, rather than the file name of the input file. In your case, the correct command line should be :
pFindSplit.exe W:\pFind\Data\EischenC\20-L014\Combined\result\pFind.protein
(The input file pFind.protein should include its path, rather than the file name only)
Now, I have updated the tool pFindSplit to add a new parameter "output foler" to avoid this bug.

You can use the latest version (pFindSplit_release20200519.zip) in the website (https://sourceforge.net/projects/panda-tools/). I also update the readme to show the detailed usage of this tool.

Feel free to contact me if you have any question or suggestion.

Cheng.