MSFragger Results Folder Reader

[mzhastings]

Implemented method to more efficiently access MsFragger results using the full results folder rather than accessing each psm.tsv file within the folder individually.

Main

• MsFraggerCombinedResults uses the path to the folder generated by MsFragger to collectively access the results from every psm.tsv file in the folder and concatenate them into one complete list of results.

Result Files

• ExperimentAnnotation and ExperimentAnnotationFile enable reading of the expriment_annotation.tsv file produced in the MsFragger results folder. This file contains the file path to each raw result file and their corresponding sample names, which are both necessary for locating the psm.tsv files.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 92.85714% with 8 lines in your changes missing coverage. Please review.

Project coverage is 75.59%. Comparing base (983c3b0) to head (49a5149).

Files with missing lines	Patch %	Lines
...nalResults/ResultFiles/MsFraggerCombinedResults.cs	92.30%	4 Missing and 2 partials :warning:
...nalResults/ResultFiles/ExperimentAnnotationFile.cs	89.47%	1 Missing and 1 partial :warning:

Additional details and impacted files

[](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #792 +/- ## ========================================== + Coverage 75.52% 75.59% +0.06% ========================================== Files 202 205 +3 Lines 30945 31057 +112 Branches 3129 3142 +13 ========================================== + Hits 23371 23477 +106 - Misses 7040 7044 +4 - Partials 534 536 +2 ``` | [Files with missing lines](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...ts/IndividualResultRecords/ExperimentAnnotation.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FIndividualResultRecords%2FExperimentAnnotation.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvSW5kaXZpZHVhbFJlc3VsdFJlY29yZHMvRXhwZXJpbWVudEFubm90YXRpb24uY3M=) | `100.00% <100.00%> (ø)` | | | [...rs/ExternalResults/ResultFiles/MsFraggerPsmFile.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FResultFiles%2FMsFraggerPsmFile.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvUmVzdWx0RmlsZXMvTXNGcmFnZ2VyUHNtRmlsZS5jcw==) | `100.00% <ø> (+5.26%)` | :arrow_up: | | [mzLib/Readers/Util/SupportedFileTypes.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&filepath=mzLib%2FReaders%2FUtil%2FSupportedFileTypes.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9VdGlsL1N1cHBvcnRlZEZpbGVUeXBlcy5jcw==) | `97.59% <100.00%> (+0.09%)` | :arrow_up: | | [...nalResults/ResultFiles/ExperimentAnnotationFile.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FResultFiles%2FExperimentAnnotationFile.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvUmVzdWx0RmlsZXMvRXhwZXJpbWVudEFubm90YXRpb25GaWxlLmNz) | `89.47% <89.47%> (ø)` | | | [...nalResults/ResultFiles/MsFraggerCombinedResults.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/792?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FResultFiles%2FMsFraggerCombinedResults.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvUmVzdWx0RmlsZXMvTXNGcmFnZ2VyQ29tYmluZWRSZXN1bHRzLmNz) | `92.30% <92.30%> (ø)` | |