Toppic search result reading (#735)

* Added in ability to parse TopPIC search result files * Added ability to write entire header * Added comments * Excluded Test class from code coverage * Adjusted some fields to match ours better * Handled a few edge cases * Added support for TopPIC version 1.5.3 * Added support for TopPIC version 1.5.3 * Fixed up operators --------- Co-authored-by: Nic Bollis <nbollis@wisc.edu> Co-authored-by: trishorts <mshort@chem.wisc.edu>
smith-chem-wisc · Nov 27, 2023 · 353ae25 · 353ae25
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diff --git a/mzLib/Readers/ExternalResults/IndividualResultRecords/ToppicPrsm.cs b/mzLib/Readers/ExternalResults/IndividualResultRecords/ToppicPrsm.cs
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+using System.Globalization;
+using System.Text;
+using System.Text.RegularExpressions;
+using CsvHelper.Configuration;
+using CsvHelper.Configuration.Attributes;
+using MassSpectrometry;
+using static System.Net.Mime.MediaTypeNames;
+
+namespace Readers;
+
+/// <summary>
+/// Class Representing a TopPIC prsm or proteoform
+/// For supported versions and software this file type can come from see
+///     Readers.ExternalResources.SupportedVersions.txt
+/// </summary>
+/// <remarks>
+/// Things that could be done to improve compatibility:
+/// Convert Variable Modifications to a list of Modification objects
+/// Convert NTerminalForm to a Modification object
+/// </remarks>
+public class ToppicPrsm
+{
+    [Ignore]
+    public static CsvConfiguration CsvConfiguration => new CsvConfiguration(CultureInfo.InvariantCulture)
+    {
+        Encoding = Encoding.UTF8,
+        HasHeaderRecord = true,
+        Delimiter = "\t",
+    };
+
+    public ToppicPrsm()
+    {
+        AlternativeIdentifications = new List<AlternativeToppicId>();
+    }
+
+    private string? _fileNameWithoutExtension;
+    [Ignore]
+    public string FileNameWithoutExtension => _fileNameWithoutExtension ??= Path.GetFileNameWithoutExtension(FilePath);
+
+    [Name("Data file name")]
+    public string FilePath { get; set; }
+
+    [Name("Prsm ID")]
+    public int PrsmID { get; set; }
+
+    [Name("Spectrum ID")]
+    public int SpectrumId { get; set; }
+
+    [Name("Fragmentation")]
+    public DissociationType DissociationType { get; set; }
+
+    [Name("Scan(s)")]
+    public int OneBasedScanNumber { get; set; }
+
+    [Name("Retention time")]
+    public double RetentionTime { get; set; }
+
+    [Name("#peaks")]
+    public int PeakCount { get; set; }
+
+    [Name("Charge")]
+    public int PrecursorCharge { get; set; }
+
+    [Name("Precursor mass")]
+    public double PrecursorMass { get; set; }
+
+    [Name("Adjusted precursor mass")]
+    public double AdjustedPrecursorMass { get; set; }
+
+    [Name("Proteoform ID")]
+    public double ProteoformId { get; set; }
+
+    [Name("Feature intensity")]
+    [Format("#.00#E+00")]
+    public double FeatureIntensity { get; set; }
+
+    [Name("Feature score")]
+    public double FeatureScore { get; set; }
+
+    [Name("Feature apex time")]
+    public double FeatureApexTime { get; set; }
+
+    [Name("#Protein hits")]
+    public int ProteinHitsCount { get; set; }
+
+    [Name("Protein accession")]
+    public string ProteinAccession { get; set; }
+
+    [Name("Protein description")]
+    public string ProteinDescription { get; set; }
+
+    [Name("First residue")]
+    public int FirstResidue { get; set; }
+
+    [Name("Last residue")]
+    public int LastResidue { get; set; }
+
+    [Name("Special amino acids")]
+    public string? SpecialAminoAcids { get; set; }
+
+    [Ignore]
+    private string? _baseSequence;
+
+    [Optional]
+    [Name("Database protein sequence")]
+    public string BaseSequence
+    {
+        get => _baseSequence ??= GetBaseSequenceFromFullSequence();
+        set => _baseSequence = value;
+    }
+
+    [Name("Proteoform")]
+    public string FullSequence { get; set; }
+
+    [Name("Proteoform mass")]
+    public double FullSequenceMass { get; set; }
+
+    [Name("Protein N-terminal form")]
+    public string ProteinNTerminalForm { get; set; }
+
+    [Optional]
+    [Name("Fixed PTMs")]
+    public string? FixedPTMs { get; set; }
+
+    [Name("#unexpected modifications")]
+    public int UnexpectedModificationsCount { get; set; }
+
+    /// <summary>
+    /// The mass shift of the mod and its semi-localization
+    /// -47:[10-14] means a mass shift of -47 Da, and the semi-localization is between the 10th and 14th amino acids
+    /// </summary>
+    [Optional]
+    [Name("unexpected modifications")]
+    public string UnexpectedModifications { get; set; }
+
+    [Name("#variable PTMs")]
+    public int VariableModificationsCount { get; set; }
+
+    [Optional]
+    [Name("variable PTMs")]
+    public string VariableModifications { get; set; }
+
+    [Name("MIScore")]
+    [TypeConverter(typeof(DashToNullOrDoubleConverter))]
+    public double? MIScore { get; set; }
+
+    [Name("#matched peaks")]
+    public int MatchedPeaksCount { get; set; }
+
+    [Name("#matched fragment ions")]
+    public int MatchedFragmentIonsCount { get; set; }
+
+    [Name("E-value")]
+    [Format("0.00E+00")]
+    public double EValue { get; set; }
+
+    [Name("Spectrum-level Q-value")]
+    [TypeConverter(typeof(DashToNullOrDoubleConverter))]
+    public double? QValueSpectrumLevel { get; set; }
+
+    [Name("Proteoform-level Q-value")]
+    [TypeConverter(typeof(DashToNullOrDoubleConverter))]
+    public double? QValueProteoformLevel { get; set; }
+
+    [Ignore]
+    public List<AlternativeToppicId> AlternativeIdentifications { get; set; }
+
+    public string GetBaseSequenceFromFullSequence()
+    {
+        // Remove text within square brackets
+        var text = Regex.Replace(FullSequence, @"\[[^\]]*\]", "");
+
+        // Remove parentheses
+        text = Regex.Replace(text, @"[()]", "");
+
+        // Remove periods
+        text = Regex.Replace(text, @"(^[^.]+)|(\.[^.]+$)", "")
+            .Replace(".","");
+        return text;
+    }
+}
+
+/// <summary>
+/// Class representing an alternative Identification from the tsv file. 
+/// </summary>
+public class AlternativeToppicId
+{
+    public int PrsmId { get; set; }
+    public string Accession { get; set; }
+    public string ProteinDescription { get; set; }
+    public int FirstResidue { get; set; }
+    public int LastResidue { get; set; }
+
+    public AlternativeToppicId(int prsmId, string accession, string proteinDescription, int firstResidue,
+        int lastResidue)
+    {
+        PrsmId = prsmId;
+        Accession = accession;
+        ProteinDescription = proteinDescription;
+        FirstResidue = firstResidue;
+        LastResidue = lastResidue;
+    }
+
+    public override string ToString()
+    {
+        return $"{PrsmId}\t\t\t\t\t\t\t\t\t\t\t\t\t\t{Accession}\t{ProteinDescription}\t{FirstResidue}\t{LastResidue}\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t";
+    }
+}