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Biobix / proBAMconvert

proBAMconvert, a conversion tool for peptide identification files (MzIdentML,pepXML,mzTAB) to the proBAM format
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Modification error after converting #8

Closed KaiLiCn closed 7 years ago

KaiLiCn commented 7 years ago

Hi:

When I parsing proBam files which were converted by proBAMconvert, I found some modification error. It lost the location detail, because all modifications I got were 1st site, such as 0-UNIMOD:4;0-UNIMOD:35 . However this issue was only found in mzIdentML converting case.

The mzIdentML files were download from pride as your suggestion, such as PXD001524 and PXD000764. Meanwhile, the parameters were set up according to your tutorial.

Kai.

vladie0 commented 7 years ago

Dear KaiLiCn,

I investigate the error, and you are right. There was a parsing error in the MzIdentML parsing where the location was wrongly extracted in certain scenarios.

This has now been fixed (pushed to GitHub), I will create patched executables shortly.

Thank you for bringing this issue to our attention, vladie0

KaiLiCn commented 7 years ago

Dear vladie0,

Thanks for your updating, I will try new version!

Best regards!

Kai

vladie0 commented 7 years ago

Apologies for the late reply,

which operating system do you use ? I want to provide you a prototype version to verify whether the application is working as intended

Kind regards, Vladie

KaiLiCn commented 7 years ago

Thank you very much, my OS is windows 10.

Best regards!

Kai

vladie0 commented 7 years ago

Dear KaiLiCn,

Can you verify whether the following version of proBAMconvert solves your issues ? https://drive.google.com/open?id=0B3z-MmiBk77oZE5pSENFRW9YSjg

Thank you

KaiLiCn commented 7 years ago

Dear Vladie0,

I tried new version of proBAMconvert, and I have got modifications. But, there is a little bug I think you might need to fix it.

I guess the modifications are from mzIdentML, so I compared them. If there is only one single modification in a peptide, the modification is same in these two files. However, when there are multi ones in a peptide, the modifications may replicate on some sites. There are two examples as follow, I list two peptides about their modification in proBAM and mzIdentML file.

proBAM: The type is XM and value is 18-UNIMOD:4 The type is XP and value is HQPQEFPTYVEPTNDEICEAFR mzIdentML:

HQPQEFPTYVEPTNDEICEAFR

proBAM: The type is XM and value is 4-UNIMOD:4;17-UNIMOD:4;17-UNIMOD:4 The type is XP and value is RMPCAEDYLSVVLNQLCVLHEK mzIdentML:

RMPCAEDYLSVVLNQLCVLHEK

I tested two files and they have same problem. I wish it may help you to fix it.

Best regards!

Kai

vladie0 commented 7 years ago

Dear Kai,

Thank you for bringing this up, I'm implementing a fix now and will send you a new executable to test ASAP.

Best Regards, Vladie

vladie0 commented 7 years ago

Dear Kai,

The following link contains a patched Windows executable . https://drive.google.com/open?id=0B3z-MmiBk77oZE5pSENFRW9YSjg

Please let me know whether this version solves your issues, once verified I'll push to public. Thank you for your collaboration! Vladie0

KaiLiCn commented 7 years ago

Dear Vladie0,

I tested this version and it solved my problem perfectly.

Thanks for your help!

Best regards!

Kai

vladie0 commented 7 years ago

Dear Kai,

I'm glad it's fixed now, thank you for helping improve proBAMconvert. If I you experience any other issues, please let us know. proBAMconvert was only recently publicly released and we're continuously looking to improve our software.

Kind Regards, Vladie0