Msangel compatibility #543
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also, I still have to make the python file for testing parameter parsing. |
proteobench/io/params/__init__.py
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| @@ -89,6 +89,6 @@ class ProteoBenchParameters: | |||
| max_precursor_charge: Optional[int] = None | |||
| scan_window: Optional[int] = None # DIA-specific | |||
| quantification_method: Optional[str] = None | |||
| second_pass: Optional[bool] = None # DIANN specific | |||
| second_pass: Optional[bool] = None # used in both DDA and DIA: same thing? | |||
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well, yes. It is not "DIANN specific", so I changed the comment.
I am sorry the new comment is not super clear. I just was not sure that it is exactly the same thing for dia and dda. But within each, I think that "second pass" is understandable. So it wont be an issue when we have module-specific parameters.
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It is DIA specific though isnt it?
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well, we also say "two-pass search" (in MQ, X!Tandem, maybe others...) when we do two successive searches with different tolerances.
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and it is a good parameter to have (I thought we did) in DDA
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... And I just realised! I forgot to add the "hidden modifications of X!Tandem" |
Co-authored-by: Henry Webel <[email protected]>
I fully agree. I think that I can maybe add a few with David's help. But I am not sure how much we'll cover actually. |
…h/ProteoBench into msangel-compatibility
| @@ -93,7 +93,10 @@ def test_flatten_of_dicts(dict_in, list_expected): | |||
| assert actual == list_expected | |||
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| parameters = [(fname, fname.with_suffix(".csv")) for fname in mqpar_fnames] | |||
| # TODO the test is broken, partly due to the expected files being incorrect | |||
| # TODO skip for now, fix in future | |||
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you can make an issue and assign me... It was hacky from the start
| assert actual.equals(expected) | ||
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| parameters = [(fname, (fname.parent / (fname.stem + "_sel.json"))) for fname in mqpar_fnames] | ||
| # TODO the test is broken, partly due to the expected files being incorrect |
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null changed to NaN - could be the issue (None vs NaN). but could be good to normalize that.
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@enryH thank you for already looking, but I need to fix a lot here still ;) |
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Seems to be working with manual input! |
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Ok, everything seems to be working! Only thing that is left to do is indicate manually changed params in the PR. |
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Ok, it works! I am going to merge with main, we can do a little bit of testing and release a new version.
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Parameter parsing of MSAngel json files for Mascot searches.
The parsing will be a bit different with other search engines (like X!Tandem - see file
test/params/MSAngel_Xtandem-export-param.json). I am working on it!