public void TestFeatureId()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string dataSet = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3";
if (!File.Exists(dataSet))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, dataSet);
}
// Feature: 5236-5286 6-12 8480.3681 5
const int minScanNum = 5236;
const int maxScanNum = 5286;
const double featureMass = 8480.3681;
//const int minScanNum = 7251;
//const int maxScanNum = 7326;
//const double featureMass = 32347.18;
// const int minScanNum = 4451;
// const int maxScanNum = 4541;
// const double featureMass = 31267.95;
var tolerance = new Tolerance(10);
var relaxedTolerance = new Tolerance(20);
const int minTagLength = 5;
const int minMergedTagLength = 7;
const int minNumTagMatches = 1;
var rawFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".raw");
var run = PbfLcMsRun.GetLcMsRun(rawFileName);
var aminoAcidSet = AminoAcidSet.GetStandardAminoAcidSet();
var featureFileName = MassSpecDataReaderFactory.ChangeExtension(dataSet, ".ms1ft");
var filter = new Ms1FtFilter(run, tolerance, featureFileName);
var ms2ScanNums =
filter.GetMatchingMs2ScanNums(featureMass)
.Where(scanNum => scanNum > minScanNum && scanNum < maxScanNum)
.ToArray();
const string tagFileName = dataSet + ".seqtag"; //"_MinLength3.seqtag"; //Path.ChangeExtension(dataSet, ".seqtag");
const string fastaFilePath = @"H:\Research\QCShew_TopDown\Production\ID_002216_235ACCEA.fasta";
if (!File.Exists(fastaFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, fastaFilePath);
}
var fastaDb = new FastaDatabase(fastaFilePath);
var searchableDb = new SearchableDatabase(fastaDb);
var tagParser = new SequenceTagParser(tagFileName, minTagLength);
var proteinsToTags = new Dictionary<string, IList<MatchedTag>>();
foreach (var ms2ScanNum in ms2ScanNums)
{
var tags = tagParser.GetSequenceTags(ms2ScanNum);
foreach (var tag in tags)
{
var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray();
foreach (var index in matchedIndices)
{
var protein = fastaDb.GetProteinName(index);
var startIndex = fastaDb.GetZeroBasedPositionInProtein(index);
var matchedTag = new MatchedTag(tag, startIndex, featureMass);
IList<MatchedTag> existingTags;
if (proteinsToTags.TryGetValue(protein, out existingTags))
{
existingTags.Add(matchedTag);
}
else
{
proteinsToTags.Add(protein, new List<MatchedTag> { matchedTag });
}
}
}
}
foreach (var entry in proteinsToTags.OrderByDescending(e => e.Value.Count))
{
if (entry.Value.Count < minNumTagMatches) break;
var proteinName = entry.Key;
var proteinSequence = fastaDb.GetProteinSequence(proteinName);
var protein = new Sequence(proteinSequence, aminoAcidSet);
Console.WriteLine(proteinName + "\t" + entry.Value.Count);
var matchedTagSet = new MatchedTagSet(proteinSequence, aminoAcidSet,
tolerance, relaxedTolerance);
Console.WriteLine("********** Before merging");
foreach (var matchedTag in entry.Value)
{
var seq = proteinSequence.Substring(matchedTag.StartIndex,
matchedTag.EndIndex - matchedTag.StartIndex);
var nTermMass = protein.GetMass(0, matchedTag.StartIndex);
var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count);
Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}",
(matchedTag.NTermFlankingMass - nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex,
matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);
matchedTagSet.Add(matchedTag);
}
Console.WriteLine("********** After merging");
foreach (var matchedTag in matchedTagSet.Tags)
{
if (matchedTag.Length < minMergedTagLength) continue;
var seq = proteinSequence.Substring(matchedTag.StartIndex,
matchedTag.EndIndex - matchedTag.StartIndex);
var nTermMass = protein.GetMass(0, matchedTag.StartIndex);
var cTermMass = protein.GetMass(matchedTag.EndIndex, protein.Count);
Console.WriteLine("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}",
(matchedTag.NTermFlankingMass-nTermMass), seq, (matchedTag.CTermFlankingMass - cTermMass), matchedTag.StartIndex,
matchedTag.IsNTermFlankingMassReliable, matchedTag.IsCTermFlankingMassReliable);
}
break;
}
}
public static Dictionary<string, MatchedTagSet> GetProteinToMatchedTagsMap(
IEnumerable<SequenceTag> tags,
SearchableDatabase searchableDb,
AminoAcidSet aaSet,
Tolerance tolerance,
Tolerance relaxedTolerance)
{
var fastaDb = searchableDb.FastaDatabase;
var proteinsToTags = new Dictionary<string, MatchedTagSet>();
foreach (var tag in tags)
{
var matchedIndices = searchableDb.FindAllMatchedSequenceIndices(tag.Sequence).ToArray();
if (matchedIndices.Length > MaxNumProteinMatchesPerTag) continue;
foreach (var index in matchedIndices)
{
var proteinName = fastaDb.GetProteinName(index);
var startIndex = fastaDb.GetZeroBasedPositionInProtein(index);
var mass = aaSet.GetComposition(tag.Sequence).Mass;
var matchedTag = new MatchedTag(tag, startIndex) { Mass = mass };
MatchedTagSet existingMatchedTagSet;
if (proteinsToTags.TryGetValue(proteinName, out existingMatchedTagSet))
{
existingMatchedTagSet.Add(matchedTag);
}
else
{
var proteinSequence = fastaDb.GetProteinSequence(proteinName);
var matchedTagSet = new MatchedTagSet(proteinSequence, aaSet, tolerance, relaxedTolerance);
matchedTagSet.Add(matchedTag);
proteinsToTags.Add(proteinName, matchedTagSet);
}
}
}
return proteinsToTags;
}
