Filters for PSM-Peptides using Search Engine provisioning

ypriverol commented 5 years ago

Some pipelines need to filter PSMs taking into account the Search Engine provisioning (which search engines have identified the corresponding spectrum), we see two cased here:

[x] Filter Peptides that are not identified by all search engines. PR https://github.com/mpc-bioinformatics/pia/pull/123
[ ] Filter peptides identifications if the corresponding spectrum was identified with different sequences by each search engine. For example Spectrum A identified by SearchEngine A with sequence A and by Search Engine B with sequence B. We should be able to remove that case with a filter.

julianu commented 5 years ago

There is a new filter named "PSM_SET_CONTAINS_SCORE_FILTER" now (see PR #123). This works like a normal literal filter and only PSM sets containing the given score are passed on. If you require more than one (like all) scores, just add all. The test-file SearchEngineFilterTest demonstrates this in more detail.

ypriverol commented 5 years ago

I will close the issue.

julianu commented 5 years ago

No, the second task is still missing ;)

medbioinf / pia

Filters for PSM-Peptides using Search Engine provisioning #124