/// <summary>
/// Read FASTA db file.
/// </summary>
/// <param name="filePath">The path to the FASTA DB file.</param>
/// <param name="parseSequence"></param>
/// <returns>Enumerable of entries in the file.</returns>
public static IEnumerable <FastaEntry> ReadFastaFile(string filePath, bool parseSequence = false)
{
FastaEntry fastaEntry = null;
var entries = new List <FastaEntry>();
foreach (var line in File.ReadLines(filePath))
{
if (line.Length == 0)
{
continue;
}
if (line[0] == '>')
{
if (fastaEntry != null)
{
entries.Add(fastaEntry);
}
fastaEntry = new FastaEntry();
var parts = line.Split(' ');
if (parts[0].Length == 1)
{
throw new FormatException("Invalid Fasta file format.");
}
fastaEntry.ProteinName = parts[0].Substring(1, parts[0].Length - 1);
if (parts.Length > 1)
{
fastaEntry.ProteinDescription = parts[1];
}
}
else
{
fastaEntry.ProteinSequenceText += line;
}
}
if (fastaEntry != null)
{
if (parseSequence)
{
fastaEntry.ProteinSequence = new Sequence(fastaEntry.ProteinSequenceText, new AminoAcidSet());
}
entries.Add(fastaEntry);
}
return(entries);
}
/// <summary>
/// Initializes a new instance of the <see cref="SearchSettingsViewModel"/> class.
/// </summary>
/// <param name="dialogService">Dialog service for opening dialogs from view model.</param>
public SearchSettingsViewModel(IMainDialogService dialogService)
{
this.dialogService = dialogService;
SearchModes = new[] { InternalCleavageType.MultipleInternalCleavages, InternalCleavageType.SingleInternalCleavage, InternalCleavageType.NoInternalCleavage };
ToleranceUnits = new[] { ToleranceUnit.Ppm, ToleranceUnit.Mz };
SelectedSequence = string.Empty;
FastaEntries = new ReactiveList <FastaEntry>();
SequenceProteins = new FastaEntry[0];
SearchRunning = false;
FromFastaEntry = true;
FromSequence = false;
// Browse Spectrum Files Command
BrowseSpectrumFilesCommand = ReactiveCommand.Create(BrowseSpectrumFilesImplementation);
// Browse Feature Files Command
BrowseFeatureFilesCommand = ReactiveCommand.Create(BrowseFeatureFilesImplementation);
// Browse Fasta DB Files Command
BrowseFastaDbFilesCommand = ReactiveCommand.Create(BrowseFastaDbFilesImplementation);
// Browse Output Directories Command
BrowseOutputDirectoriesCommand = ReactiveCommand.Create(BrowseOutputDirectoriesImplementation);
// Select All Proteins Command
SelectAllProteinsCommand = ReactiveCommand.Create(() => SelectProteinsImplementation(true), FastaEntries.WhenAnyValue(x => x.Count).Select(count => count > 0));
// Select No Proteins Command
SelectNoProteinsCommand = ReactiveCommand.Create(() => SelectProteinsImplementation(false), FastaEntries.WhenAnyValue(x => x.Count).Select(count => count > 0));
// Manage Modifications Command
ManageModificationsCommand = ReactiveCommand.Create(ManageModificationsImplementation);
// Add Modifications Command
AddModificationCommand = ReactiveCommand.Create(AddModificationImplementation);
// Run Command - Disabled when there is no SpectrumFilePath, FastaDbFilePath, or OutputFilePath selected
RunCommand = ReactiveCommand.CreateFromTask(async _ => await RunImplementation(),
this.WhenAnyValue(
x => x.SpectrumFilePath,
x => x.FastaDbFilePath,
x => x.OutputFilePath)
.Select(x => !string.IsNullOrWhiteSpace(x.Item1) &&
!string.IsNullOrWhiteSpace(x.Item2) &&
!string.IsNullOrWhiteSpace(x.Item3))
);
// Prev tab command
PrevTabCommand = ReactiveCommand.Create(() => TabIndex--,
Observable.Merge(
new[]
{
this.WhenAnyValue(x => x.TabIndex).Select(tabIndex => tabIndex > 0),
RunCommand.IsExecuting.Select(exec => !exec)
}));
// Next tab command
NextTabCommand = ReactiveCommand.Create(() => TabIndex++,
Observable.Merge(
new[]
{
this.WhenAnyValue(x => x.TabIndex).Select(tabIndex => tabIndex < MaxTabIndex),
RunCommand.IsExecuting.Select(exec => !exec)
}));
// Cancel Command
CancelCommand = ReactiveCommand.Create(CancelImplementation);
// Default values
SelectedSearchMode = InternalCleavageType.SingleInternalCleavage;
MinSequenceLength = 21;
MaxSequenceLength = 300;
MinPrecursorIonCharge = 2;
MaxPrecursorIonCharge = 30;
MinProductIonCharge = 1;
MaxProductIonCharge = 15;
MinSequenceMass = 3000.0;
MaxSequenceMass = 50000.0;
PrecursorIonToleranceValue = 10;
PrecursorIonToleranceUnit = ToleranceUnit.Ppm;
ProductIonToleranceValue = 10;
PrecursorIonToleranceUnit = ToleranceUnit.Ppm;
minScanNumber = 0;
maxScanNumber = 0;
maxDynamicModificationsPerSequence = 0;
FixedNTerm = true;
FixedCTerm = true;
NumMatchesPerSpectrum = 1;
// When search mode is selected, display correct search mode description
this.WhenAnyValue(x => x.SelectedSearchMode)
.Subscribe(searchMode => SearchModeDescription = searchModeDescriptions[(int)searchMode]);
// When Spectrum file path is selected, use its directory for the output path by default if a output path
// has not already been selected.
this.WhenAnyValue(x => x.SpectrumFilePath)
.Where(_ => string.IsNullOrWhiteSpace(OutputFilePath))
.Select(Path.GetDirectoryName)
.Subscribe(specDir => OutputFilePath = specDir);
SearchModifications = new ReactiveList <SearchModificationViewModel> {
ChangeTrackingEnabled = true
};
this.WhenAnyValue(x => x.FastaDbFilePath).Subscribe(_ => LoadFastaFile());
this.WhenAnyValue(x => x.FastaEntries.Count, x => x.SelectedSequence)
.Select(x => FastaEntries.Where(entry => entry.ProteinSequenceText.Contains(x.Item2)).ToArray())
.Subscribe(entries => SequenceProteins = entries);
// Remove search modification when its Remove property is set to true.
SearchModifications.ItemChanged.Where(x => x.PropertyName == "Remove")
.Select(x => x.Sender).Where(sender => sender.Remove)
.Subscribe(searchMod => SearchModifications.Remove(searchMod));
ModificationsUpdated = false;
}
/// <summary>
/// Create a truncated FASTA file based on selected proteins.
/// </summary>
/// <returns>The path to the truncated FASTA database file.</returns>
private string CreateTruncatedFastaFile()
{
var fastaFileName = Path.GetFileNameWithoutExtension(this.FastaDbFilePath);
var filePath = string.Format("{0}\\{1}_truncated.fasta", this.OutputFilePath, fastaFileName);
IEnumerable <FastaEntry> entries = new FastaEntry[0];
if (this.FromFastaEntry)
{
entries = this.FastaEntries.Where(entry => entry.Selected);
}
else if (this.FromSequence)
{
var selectedEntries = this.SequenceProteins.Where(entry => entry.Selected).ToArray();
if (this.FixedNTerm && this.FixedCTerm)
{ // Just use the selected sequence for every protein.
entries = selectedEntries.Select(
entry =>
new FastaEntry
{
ProteinName = entry.ProteinName,
ProteinDescription = entry.ProteinDescription,
ProteinSequenceText = this.SelectedSequence,
Selected = true
});
entries = new List <FastaEntry> {
entries.FirstOrDefault()
};
}
else if (this.FixedNTerm)
{
entries = from entry in selectedEntries
let startIndex = entry.ProteinSequenceText.IndexOf(this.SelectedSequence, StringComparison.Ordinal)
where startIndex > -1
let sequence = entry.ProteinSequenceText.Substring(startIndex)
select new FastaEntry
{
ProteinName = entry.ProteinName,
ProteinDescription = entry.ProteinDescription,
ProteinSequenceText = sequence
};
}
else if (this.FixedCTerm)
{
entries = from entry in selectedEntries
let startIndex = entry.ProteinSequenceText.IndexOf(this.SelectedSequence, StringComparison.Ordinal)
where startIndex > -1
let sequence = entry.ProteinSequenceText.Substring(0, startIndex + this.SelectedSequence.Length)
select new FastaEntry
{
ProteinName = entry.ProteinName,
ProteinDescription = entry.ProteinDescription,
ProteinSequenceText = sequence
};
}
else
{
entries = selectedEntries;
}
}
Console.WriteLine(@"Creating truncated fasta file at: {0}", filePath);
FastaReaderWriter.Write(entries, filePath);
return(filePath);
}
