singjc
commented
1 year ago Hi,
You may have to use the legacy workflow which supports TSV, pyprophet legacy workflow. Or alternatively, you could convert the SWATHAtlas TraML file to a sqlite-based PQP file, which would allow you to output an OSW file from OpenSwathWorkflow.
You can use the TargetedFileConveter tool in OpenMS, or you can use the recently implemented TargetedFileConverter shipped with the latest EasyPQP python packge
EasyPQP
easypqp targeted-file-converter --in library.TraML --out library.pqpOpenMS
TargetedFileConverter --in library.TraML --out library.pqpBest,
Justin
Hello,
I encountered an error when going from OpenSwathWorkflow into pyprophet. As some background, I have one .mzML file that I aligned with a library with the .TraML extension, not a .pqp file. The library is the one from SWATHAtlas (SAL00026). Therefore, I cannot output a .osw from OpenSwathWorkflow, so my input to pyprophet is a TSV file. Pyprophet did not throw an error at this, so I assume it is okay. After pyprophet was initiated, I got the error "AssertionError: Column group_id is not in input file(s)." I opened the TSV file that is output by OpenSwathWorkflow, and indeed the column "group_id" is not available, though there are a few others such as "id" or "transition_group_id." I am not sure if one of these is what is supposed to be read as the group id. I am using openms version 2.4.0.
I have attached the error report for the pyprophet section of my code, and the full error report from the start of OpenSwathWorkflow through pyprophet. (I ran them as one script and simply copy/pasted the pyprophet section to make it easier to find.)
Thank you for your consideration.
Regards, Andrew Sweatt
error_report_full.txt pyprophet_error_report.txt