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:books: :microscope: PIA - Protein Inference Algorithms
https://github.com/medbioinf/pia
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PSM ms_run[] get repeated in mztab export. #133

Closed ypriverol closed 10 months ago

ypriverol commented 5 years ago

For some reason PSM ms_run[] get repeated in mztab export. Here and exmaple:

PSM FGIAAK 1 P21796 0 databaseName null [MS, MS:1002387, PIA, 1.3.10]|[PSI-MS, MS:1001476, X!Tandem, X! Tandem Alanine (2017.2.1.4)]|[PSI-MS, MS:1002048, MS-GF+, Release (v2017.07.21)] 0.003638683087973093 0.0075 20.0 0.004483837330552659 115.0 1.7413855E-8 0.34254366 null 1729.1622 2 303.68479405403644 303.683456328125 ms_run[1]:index=1433|ms_run[1]:index=1433|ms_run[1]:index=1433|ms_run[2]:index=1433|ms_run[2]:index=1433|ms_run[2]:index=1433 R Y 219 224 0 0 1

ypriverol commented 5 years ago

Error found and fixed, PR pending. One questions for @julianu .

In the mztab export when you export one PSM (that is a PSMSet) that contains a list psms. We use to export all the ms_runs even if the scores are different. IS that correct @julianu see line:

https://github.com/mpc-bioinformatics/pia/blob/878f40382e2f24fab1a375ccaa0cf6504ee337d5/src/main/java/de/mpc/pia/modeller/exporter/MzTabExporter.java#L1082

julianu commented 5 years ago

This was fixed in #136, right?

ypriverol commented 5 years ago

Yes. Still you should read my comment before.

julianu commented 5 years ago

When exporting PSMSets, all scores of the PSMs of the set will be exported, yes. When using only one search engine and combining the results of multiple ms_runs, no sets need to be created (and actually should, if everything goes well, have just one PSM if sets were created.)