How to convert the output of Percolator by poutmzid?

[plantton]

I'm wondering if this tool is still active, and can be applied to the latest version of Percolator, to convert the output of Percolator into mzIdentML format?

[percolator]

Yes, the pout2mzid is still maintained. Please let me know if you have any problems running the tool.

…

On Fri, Dec 18, 2020 at 11:50 PM Chong TANG ***@***.***> wrote: I'm wondering if this tool is still active, and can be applied to the latest version of Percolator, to convert the output of Percolator into mzIdentML format? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKACNGY6ZMTFXVJ2N5BLSVPMDXANCNFSM4VBYZB2Q> .

[tivdnbos]

Since this issue was stil open, I thought I could ask it here.
I was wondering if it's also possible to go from from a percolator output file in tab separated format to an mzid file? Or, does it has to be already in xml format?

[percolator]

Unfortunately, it has to be given as a percolator pout.xml file. --Lukas

…

On Wed, Feb 17, 2021 at 5:33 PM tivdnbos ***@***.***> wrote: Since this issue was stil open, I thought I could ask it here. I was wondering if it's also possible to go from from a percolator output file in tab separated format to an mzid file? Or, does it has to be already in xml format? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKADF2AE5PUIVQS3MXH3S7PVUTANCNFSM4VBYZB2Q> .

[tivdnbos]

Thanks for the quick reply, Lukas!
Regarding that, does it require to have a pin file in XML format, or can that one still be in tab separated format? So, that I rerun percolator with as pin file a tab separated file, and ask to create a pout.xml file?

[percolator]

Yes that should work, percolator can read tab delimited files and write pout XML files.

…

On Wed, Feb 17, 2021 at 5:49 PM tivdnbos ***@***.***> wrote: Thanks for the quick reply, Lukas! Regarding that, does it require to have a pin file in XML format, or can that one still be in tab separated format? So, that I rerun percolator with as pin file a tab separated file, and ask to create a pout.xml file? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKAGHON6RRWNKQOT77RDS7PXS5ANCNFSM4VBYZB2Q> .

[tivdnbos]

Thanks!
I've been able to create .pout.xml files given a tsv pin file, but when running
pout2mzid -p <my_pout>.pout.xml
I receive the error "Segmentation fault (core dumped)". Did you receive this error message before?

[percolator]

That sounds bad. What input file did you use?

…

On Wed, Feb 17, 2021 at 7:21 PM tivdnbos ***@***.***> wrote: Thanks! I've been able to create .pout.xml files given a tsv pin file, but when running pout2mzid -p <my_pout>.pout.xml I receive the error "Segmentation fault (core dumped)". Did you receive this error message before? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKAC2B54VWFFBW2I5TFDS7QCITANCNFSM4VBYZB2Q> .

[tivdnbos]

I attached here one of the pout.xml files. To be able to upload this on github, I changed the extension from .pout.xml to .txt.

151222_NJ_Felipe_Y11_allfeatures.txt

[percolator]

No, I cannot recreate the seg.fault. However, as I do not have the mzid file you try to patch, I can only see the first part of the processing.

…

On Thu, Feb 18, 2021 at 10:29 AM tivdnbos ***@***.***> wrote: I attached here one of the pout.xml files. To be able to upload this on github, I changed the extension from .pout.xml to .txt. 151222_NJ_Felipe_Y11_allfeatures.txt <https://github.com/percolator/pout2mzid/files/6001675/151222_NJ_Felipe_Y11_allfeatures.txt> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXKADXNR2IBE45FX5PKWDS7TMXDANCNFSM4VBYZB2Q> .