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medbioinf / pia

:books: :microscope: PIA - Protein Inference Algorithms
https://github.com/medbioinf/pia
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New filter added about all psm search in all search engines. #123

Closed ypriverol closed 5 years ago

ypriverol commented 5 years ago

@julianu:

The current PR includes a new filter to filter psms that haven't been found by all search engines in the analysis. This is particularly good if we want to retrieve all the Peptide/PSMs evidence that are highly confident.

Please review the final PR and let me know what do you think.

codecov-io commented 5 years ago

Codecov Report

Merging #123 into master will increase coverage by <.01%. The diff coverage is 40.39%.

Impacted file tree graph

@@             Coverage Diff              @@
##             master     #123      +/-   ##
============================================
+ Coverage     52.43%   52.44%   +<.01%     
- Complexity     2282     2301      +19     
============================================
  Files           174      175       +1     
  Lines         17441    17517      +76     
  Branches       2860     2874      +14     
============================================
+ Hits           9146     9186      +40     
- Misses         7336     7361      +25     
- Partials        959      970      +11
Impacted Files Coverage Δ Complexity Δ
.../de/mpc/pia/intermediate/compiler/PIACompiler.java 68.7% <ø> (ø) 67 <0> (ø) :arrow_down:
...java/de/mpc/pia/modeller/exporter/CSVExporter.java 68.93% <ø> (ø) 28 <0> (ø) :arrow_down:
.../pia/modeller/protein/scoring/AbstractScoring.java 47.45% <ø> (ø) 9 <0> (ø) :arrow_down:
...c/pia/intermediate/compiler/PIASimpleCompiler.java 80.82% <ø> (ø) 27 <0> (ø) :arrow_down:
...e/mpc/pia/modeller/exporter/MzIdentMLExporter.java 73.23% <ø> (ø) 117 <0> (ø) :arrow_down:
...c/main/java/de/mpc/pia/tools/pride/PRIDETools.java 49.25% <ø> (-1.5%) 12 <0> (-1)
src/main/java/de/mpc/pia/tools/MzIdentMLTools.java 59.72% <ø> (ø) 33 <0> (ø) :arrow_down:
.../main/java/de/mpc/pia/modeller/score/FDRScore.java 92.47% <ø> (ø) 23 <0> (ø) :arrow_down:
...deller/peptide/ReportPeptideComparatorFactory.java 0% <0%> (ø) 0 <0> (ø) :arrow_down:
.../intermediate/compiler/parser/IdXMLFileParser.java 65.85% <0%> (-0.23%) 57 <2> (ø)
... and 31 more

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julianu commented 5 years ago

I am working on this. Needs some changes, as a filter directly like this does not work, but I found a solution, which I am implementing right now.