Using StPeter with Philosopher

[melechco]

Thanks for providing this great tool.
Would it be possible to incorporate StPeter into Philosopher?
Personally, I find the idea of correcting by protein length very useful.
I tried to process prot.xml (Philosopher output) with StPeter command line but it is not recognizing pepXML created by Philosopher.

Output from stpeter:
WARNING: Data file(s) in pepXML not found. Please update paths in pepXML. Attempting to open from current working directory.
ERROR: Could not read data files referenced in: xxxxx
Please update paths (preferred) or move missing data files to current working directory.

[prvst]

@melechco

I'm glad that you find the program useful.

Adding StPeter to Philosopher is not in our plannings right now, but I did a simple test here and I got it working. That error you got seems to indicate that the pepXML is in a different path, make sure that all your files are still in the same folder they were created and I'll let you know if we decide to add it to Philosopher in the future.

[anesvi]

If you used FragPipe, starting with the latest version of FragPipe it moves files to a temp folder (so we can run multiple files in parallel0 when running PeptideProphet. So the links interact.pep.xml may not be correct. I am not sure we would have an easy fix. You can try with the previous version of FragPipe to see if working in that case. From: Felipe Leprevost [mailto:notifications@github.com] Sent: Tuesday, October 08, 2019 10:29 AM To: Nesvilab/philosopher <philosopher@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: Re: [Nesvilab/philosopher] Using StPeter with Philosopher (#73) External Email - Use Caution @melechco<https://github.com/melechco> I'm glad that you find the program useful. Adding StPeter to Philosopher is not in our plannings right now, but I did a simple test here and I got it working. That error you got seems to indicate that the pepXML is in a different path, make sure that all your files are still in the same folder they were created and I'll let you know if we decide to add it to Philosopher in the future. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#73?email_source=notifications&email_token=AIIMM66OWT3XRIBZC4DSA2TQNSKJVA5CNFSM4I6KHS32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAULX5A#issuecomment-539540468>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AIIMM6YY5Q5TIZ2JXFZ5ZNTQNSKJVANCNFSM4I6KHS3Q>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Thanks Drs. Leprevost and Nesvizhskii,
I am using MSFragger2-1 so it seems that it is looking for files from the temp folder.
I will try with the previous version.
Thanks once again!