public void TestGettingProteinLengthAndPosition()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\Short.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
db.Read();
var indexedDb = new IndexedDatabase(db);
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsets(6, 20, 2, 0, Enzyme.Trypsin))
{
var annotation = peptideAnnotationAndOffset.Annotation;
var offset = peptideAnnotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}",
annotation,
offset,
db.GetProteinName(offset),
db.GetProteinLength(db.GetProteinName(offset)),
db.GetOneBasedPositionInProtein(offset) + 1);
}
}
public void TestGettingProteinLengthAndPosition()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\Short.fasta"));
var db = new FastaDatabase(fastaFile.FullName);
db.Read();
var indexedDb = new IndexedDatabase(db);
foreach (var peptideAnnotationAndOffset in indexedDb.AnnotationsAndOffsets(6, 20, 2, 0, Enzyme.Trypsin))
{
var annotation = peptideAnnotationAndOffset.Annotation;
var offset = peptideAnnotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}",
annotation,
offset,
db.GetProteinName(offset),
db.GetProteinLength(db.GetProteinName(offset)),
db.GetOneBasedPositionInProtein(offset) + 1);
}
}
public void CreateTargetList()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string databaseFilePath = @"D:\Research\Data\IPRG2014\database\SpikedInPeptides.fasta";
if (!File.Exists(databaseFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, databaseFilePath);
}
var database = new FastaDatabase(databaseFilePath);
database.Read();
var indexedDatabase = new IndexedDatabase(database);
var numTargets = 0;
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
Console.WriteLine("Peptide\tFormula\tProtein");
foreach (var annotationAndOffset in indexedDatabase.AnnotationsAndOffsets(6, 30, 1, 1, Enzyme.Trypsin))
{
var annotation = annotationAndOffset.Annotation;
var peptide = annotation.Substring(2, annotation.Length - 4);
var offset = annotationAndOffset.Offset;
Console.WriteLine("{0}\t{1}\t{2}", peptide, (aaSet.GetComposition(peptide) + Composition.H2O).ToPlainString(), database.GetProteinName(offset));
numTargets++;
}
Console.WriteLine("NumTargets: {0}", numTargets);
}
private IEnumerable <AnnotationAndOffset> GetAnnotationsAndOffsets(FastaDatabase database)
{
var indexedDbTarget = new IndexedDatabase(database);
IEnumerable <AnnotationAndOffset> annotationsAndOffsets;
if (NumTolerableTermini == 0)
{
annotationsAndOffsets = indexedDbTarget.AnnotationsAndOffsetsNoEnzyme(MinSequenceLength, MaxSequenceLength);
}
else
{
annotationsAndOffsets = indexedDbTarget.AnnotationsAndOffsets(MinSequenceLength, MaxSequenceLength,
NumTolerableTermini, 2, Enzyme);
}
return(annotationsAndOffsets);
}
private static void TestCountingPeptides()
{
var aaSet = new AminoAcidSet();
var sw = new Stopwatch();
sw.Start();
//const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002166_F86E3B2F.fasta";
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_003456_9B916A8B.fasta";
// const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_004208_295531A4.fasta";
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
indexedDb.Read();
//var numPeptides = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 150).LongCount();
var peptides =
indexedDb.AnnotationsAndOffsets(7, 40, 2, 2, Enzyme.Trypsin);
Parallel.ForEach(peptides, annotationAndOffset =>
//foreach(var annotationAndOffset in peptides)
{
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
var graph = SequenceGraph.CreateGraph(aaSet, annotation);
}
)
;
// Console.WriteLine("NumPeptides: {0}", numPeptides);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"{0:f4} sec", sec);
}
public void TestRunningTimeChromGen()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rafFilePath = @"C:\cygwin\home\kims336\Data\QCShewQE\QC_Shew_13_04_A_17Feb14_Samwise_13-07-28.raf";
if (!File.Exists(rafFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rafFilePath);
}
var rafRun = new PbfLcMsRun(rafFilePath);
var tolerance = new Tolerance(10);
const string dbFile = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.fasta";
if (!File.Exists(dbFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dbFile);
}
var db = new FastaDatabase(dbFile);
var indexedDb = new IndexedDatabase(db);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var numPeptides = 0;
foreach (var peptide in indexedDb.AnnotationsAndOffsets(6, 30, 2, 2, Enzyme.Trypsin))
{
++numPeptides;
var comp = new Sequence(peptide.Annotation.Substring(2, peptide.Annotation.Length - 4), aaSet).Composition + Composition.H2O;
var mz = new Ion(comp, 2).GetMonoIsotopicMz();
//Console.WriteLine(peptide.Annotation + " " + mz);
rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic1 = run.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//var xic2 = rafRun.GetFullPrecursorIonExtractedIonChromatogram(mz, tolerance);
//Assert.True(xic1.Count == xic2.Count);
//for (var i = 0; i < xic1.Count; i++)
//{
// if (!xic1[i].Equals(xic2[i]))
// {
// Console.WriteLine("{0} {1} {2}", i, xic1[i], xic2[i]);
// }
// Assert.True(xic1[i].Equals(xic2[i]));
//}
if (numPeptides == 100000)
{
break;
}
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}