public void TestEnumeratingProteins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
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);
var indexedDb = new IndexedDatabase(db);
foreach (var annotationAndOffset in indexedDb.IntactSequenceAnnotationsAndOffsetsWithCTermCleavagesLargerThan(100, 300, 3))
{
Console.WriteLine(annotationAndOffset.Annotation);
}
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestEnumeratingProteins()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\Short.fasta"));
var db = new FastaDatabase(fastaFile.FullName);
var indexedDb = new IndexedDatabase(db);
var numPeptides = 0;
foreach (var annotationAndOffset in indexedDb.IntactSequenceAnnotationsAndOffsetsWithCTermCleavagesLargerThan(100, 300, 3))
{
if (numPeptides < 20)
{
Console.WriteLine(annotationAndOffset.Annotation);
}
numPeptides++;
}
sw.Stop();
Console.WriteLine("Peptide count: {0}", numPeptides);
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestCountingProteoformsCloseToNTermOrCTerm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minSequenceLength = 21; // 21
const int maxSequenceLength = 300; // 300
const int maxNumNTermCleavages = 1;
const int maxNumCTermCleavages = 0;
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
//const string dbFile = @"C:\cygwin\home\kims336\Data\TopDownQCShew\database\ID_002216_235ACCEA.fasta";
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);
var indexedDb = new IndexedDatabase(db);
var both = 0L;
var nTermOnly = 0L;
var cTermOnly = 0L;
foreach (
var annotationAndOffset in
indexedDb.IntactSequenceAnnotationsAndOffsets(minSequenceLength, int.MaxValue,
maxNumCTermCleavages))
{
// numCTermCleavages <= maxNumCTermCleavages
var annotation = annotationAndOffset.Annotation;
var length = (annotation.Length - 4);
var numNTermCleavage = 0;
int cleavedLength;
while ((cleavedLength = length - numNTermCleavage) >= minSequenceLength)
{
if (cleavedLength <= maxSequenceLength)
{
if (numNTermCleavage <= maxNumNTermCleavages)
{
++both;
}
else
{
++cTermOnly;
}
var anno = numNTermCleavage == 0
? annotation
: string.Format("{0}.{1}", annotation[1 + numNTermCleavage], annotation.Substring(2 + numNTermCleavage));
Console.WriteLine(anno);
}
++numNTermCleavage;
}
}
foreach (
var annotationAndOffset in
indexedDb.IntactSequenceAnnotationsAndOffsetsWithCTermCleavagesLargerThan(minSequenceLength, int.MaxValue,
maxNumCTermCleavages))
{
// numCTermCleavages > maxNumCTermCleavages
var annotation = annotationAndOffset.Annotation;
var length = (annotation.Length - 4);
for (var numNTermCleavage = 0; numNTermCleavage <= maxNumNTermCleavages; numNTermCleavage++)
{
var cleavedLength = length - numNTermCleavage;
if (cleavedLength >= minSequenceLength && cleavedLength <= maxSequenceLength)
{
++nTermOnly;
var anno = numNTermCleavage == 0
? annotation
: string.Format("{0}.{1}", annotation[1 + numNTermCleavage], annotation.Substring(2 + numNTermCleavage));
Console.WriteLine(anno);
}
}
}
Console.WriteLine("Both: {0}", both);
Console.WriteLine("N-term only: {0}", nTermOnly);
Console.WriteLine("C-term only: {0}", cTermOnly);
Console.WriteLine("All: {0}", both + nTermOnly + cTermOnly);
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestCountingProteoformsCloseToNTermOrCTerm()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const int minSequenceLength = 21; // 21
const int maxSequenceLength = 300; // 300
const int maxNumNTermCleavages = 1;
const int maxNumCTermCleavages = 0;
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
var fastaFile = Utils.GetTestFile(methodName, Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"MSPathFinderT\Short.fasta"));
var db = new FastaDatabase(fastaFile.FullName);
var indexedDb = new IndexedDatabase(db);
var both = 0L;
var nTermOnly = 0L;
var cTermOnly = 0L;
var displayedResults = 0;
foreach (
var annotationAndOffset in
indexedDb.IntactSequenceAnnotationsAndOffsets(minSequenceLength, int.MaxValue,
maxNumCTermCleavages))
{
// numCTermCleavages <= maxNumCTermCleavages
var annotation = annotationAndOffset.Annotation;
var length = (annotation.Length - 4);
var numNTermCleavage = 0;
int cleavedLength;
while ((cleavedLength = length - numNTermCleavage) >= minSequenceLength)
{
if (cleavedLength <= maxSequenceLength)
{
if (numNTermCleavage <= maxNumNTermCleavages)
{
++both;
}
else
{
++cTermOnly;
}
var anno = numNTermCleavage == 0
? annotation
: string.Format("{0}.{1}", annotation[1 + numNTermCleavage], annotation.Substring(2 + numNTermCleavage));
if (displayedResults < 20)
{
Console.WriteLine(anno);
}
displayedResults++;
}
++numNTermCleavage;
}
}
displayedResults = 0;
foreach (
var annotationAndOffset in
indexedDb.IntactSequenceAnnotationsAndOffsetsWithCTermCleavagesLargerThan(minSequenceLength, int.MaxValue,
maxNumCTermCleavages))
{
// numCTermCleavages > maxNumCTermCleavages
var annotation = annotationAndOffset.Annotation;
var length = (annotation.Length - 4);
for (var numNTermCleavage = 0; numNTermCleavage <= maxNumNTermCleavages; numNTermCleavage++)
{
var cleavedLength = length - numNTermCleavage;
if (cleavedLength >= minSequenceLength && cleavedLength <= maxSequenceLength)
{
++nTermOnly;
var anno = numNTermCleavage == 0
? annotation
: string.Format("{0}.{1}", annotation[1 + numNTermCleavage], annotation.Substring(2 + numNTermCleavage));
if (displayedResults < 20)
{
Console.WriteLine(anno);
}
displayedResults++;
}
}
}
Console.WriteLine("Both: {0}", both);
Console.WriteLine("N-term only: {0}", nTermOnly);
Console.WriteLine("C-term only: {0}", cTermOnly);
Console.WriteLine("All: {0}", both + nTermOnly + cTermOnly);
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}