Transcriptomics Digestion and Fragmentation #801
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Alexander-Sol
requested changes
Sep 23, 2024
There was a problem hiding this comment.
Mostly minor quibbles, but a couple things that were confusing enough that I don't want to approve just yet
- NucleicAcid.Equals() doesn't check the sequence
- NucleicAcid.ParseSequence() does several things that I wouldn't suspect based on the name
- OligoWithSetMods termini setters modify multiple different fields.
added 5 commits
September 24, 2024 14:30
Introduced support for handling RNA data within the UsefulProteomicsDatabases project. Key changes include: - Added `Transcriptomics\TestData` folder to `Test.csproj`. - Changed access modifiers in `ProteinDbLoader.cs` to internal. - Added `using` directives for `Transcriptomics` in `ProteinXmlEntry.cs`. - Introduced methods `ParseRnaEndElement` and `ParseRnaEntryEndElement` in `ProteinXmlEntry.cs`. - Modified `ParseAnnotatedMods` to check for RNA modifications. - Added project reference to `Transcriptomics.csproj` in `UsefulProteomicsDatabases.csproj`. - Added `ClassExtensions.cs` with `CreateNew` method for nucleic acids. - Added `RnaDbLoader.cs` for RNA database loading. - Added `RnaDecoyGenerator.cs` for generating decoy RNA sequences.
Updated `using` directives in `TestDigestion.cs` and `OligoWithSetMods.cs` to include necessary namespaces. Added assertions in `TestDigestion.cs` for `SequenceWithChemicalFormulas` and `FullSequenceWithMassShift`. Changed `namespace` in `OligoWithSetMods.cs` to `Transcriptomics.Digestion`. Implemented and cached `SequenceWithChemicalFormulas` property in `OligoWithSetMods.cs`.
- Added new files `ModomicsUnmodifiedTrimmed.fasta` and `ModomicsUnmodifiedTrimmed.fasta.gz` to `Test.csproj` with `CopyToOutputDirectory` set to `PreserveNewest`. - Removed the `Transcriptomics\TestData` folder from `Test.csproj`. - Introduced `Transcribe` method in `ClassExtensions.cs` for DNA to RNA transcription. - Added summary comment to `NucleolyticOligo` class in `NucleolyticOligo.cs`. - Added `ApplyRegex` method in `FastaHeaderFieldRegex.cs`. - Introduced `ProteinDbWriter` class in `ProteinDbWriter.cs` for writing protein and nucleic acid databases. - Modified `GetModsForThisProtein` to `GetModsForThisBioPolymer` in `ProteinDbWriter.cs`. - Added `RnaDbLoader` class in `RnaDbLoader.cs` for RNA FASTA header detection and sequence loading. - Updated user dictionary in `mzLib.sln.DotSettings` with new terms. - Added test cases in `TestDbLoader.cs` for RNA database loading and header detection. - Introduced `TestDecoyGeneration` class in `TestDecoyGenerator.cs` for RNA decoy generation tests. - Added RNA sequence file `ModomicsUnmodifiedTrimmed.fasta` and its compressed version.
- Added `using` directives for `Transcriptomics.Digestion` and `UsefulProteomicsDatabases.Transcriptomics` in `TestDecoyGenerator.cs`. - Introduced `TestCreateNew` in `TestDecoyGenerator.cs` to verify RNA and oligo creation. - Added `using` directive for `MzLibUtil` in `TestDigestion.cs`. - Added a test in `TestDigestion.cs` for exception handling with invalid sequences. - Added `using` directives for `Omics` and related namespaces in `TestFragmentation.cs`. - Modified `TestFragmentation_Modified` in `TestFragmentation.cs` to use `OligoWithSetMods` directly and added assertions. - Updated `ClassExtensions.cs` to allow setting `isDecoy` in new `RNA` objects. - Refactored `OligoWithSetMods.cs` to return a dictionary from `GetModsAfterDeserialization`. - Updated `OligoWithSetMods.cs` to initialize `_allModsOneIsNterminus` using the returned dictionary.
trishorts
reviewed
Sep 25, 2024
trishorts
reviewed
Sep 25, 2024
trishorts
reviewed
Sep 26, 2024
trishorts
reviewed
Sep 26, 2024
trishorts
reviewed
Sep 26, 2024
trishorts
reviewed
Sep 26, 2024
trishorts
reviewed
Oct 1, 2024
Refactored constructors, improved exception handling, and added comprehensive tests across multiple files. Key changes include: - `MzLibException.cs`: Updated constructor to include `innerException`. - `TestDecoyGenerator.cs`: Added assertions for `CreateNew` method. - `TestDigestion.cs`: Added assertions and new test for RNA digestion exception. - Refactored modification lists and added various tests for modifications. - `TestNucleicAcid.cs`: Refactored methods, adjusted precision, and updated terminus assignments. - `NucleolyticOligo.cs`: Changed parameter types, updated comments, and improved variable names. - `OligoWithSetMods.cs`: Enhanced exception messages and updated modification location checks. - `NucleicAcid.cs`: Added `using` directive, changed exception type, and refactored methods. - `mzLib.sln.DotSettings`: Updated user dictionary entries.
…into RnaImplementation
Added new test data files (`20mer1.fasta`, `20mer1.fasta.gz`, `20mer1.xml`, `20mer1.xml.gz`) to the `Transcriptomics\TestData` directory in the `Test.csproj` file, ensuring they are copied to the output directory. Introduced `TestDbReadingDifferentExtensions` in `TestDbLoader.cs` to verify RNA database reading from various formats. Added `TestDigestionMaxIsoforms` in `TestDigestion.cs` to test RNA sequence digestion with max isoforms. Updated `WriteNucleicAcidXmlDatabase` in `ProteinDbWriter.cs` with remarks for future implementation. Added a TODO in `RnaDecoyGenerator.cs` regarding palindromic sequences' impact on fragment ions. Included new RNA sequence data in test files for validation.
Alexander-Sol
previously approved these changes
Oct 3, 2024
trishorts
approved these changes
Oct 10, 2024
elaboy
approved these changes
Oct 14, 2024
Alexander-Sol
approved these changes
Oct 15, 2024
elaboy
approved these changes
Oct 15, 2024
elaboy
approved these changes
Oct 15, 2024
elaboy
approved these changes
Oct 15, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Implemented the derived calasses of the Omics abstracts and interfaces for RNA