private void WriteResultsToFile(DatabaseSequenceSpectrumMatch[] matches, string outputFilePath, FastaDatabase database)
{
using (var writer = new StreamWriter(outputFilePath))
{
writer.WriteLine("Scan\tPre\tSequence\tPost\tModifications\tComposition\tProteinName\tProteinDesc" +
"\tProteinLength\tStart\tEnd\tCharge\tMostAbundantIsotopeMz\tMass\t#MatchedFragments\tProbability\tSpecEValue\tEValue");
foreach(var scanNum in _ms2ScanNums)
{
var match = matches[scanNum];
if (match == null) continue;
var sequence = match.Sequence;
var offset = match.Offset;
var start = database.GetOneBasedPositionInProtein(offset) + 1 + match.NumNTermCleavages;
var end = start + sequence.Length - 1;
var proteinName = database.GetProteinName(match.Offset);
var protLength = database.GetProteinLength(proteinName);
var ion = match.Ion;
var proteinDescription = database.GetProteinDescription(match.Offset);
var probability = CompositeScorer.GetProbability(match.Score);
// Note for DblToString(value, 9, true), by having "9" and "true",
// values between 100 and 999 Da will have 7 digits after the decimal place, and
// values between 1000 and 9999 will have 6 digits after the decimal place
writer.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}\t{14}\t{15}\t{16}\t{17}",
scanNum,
match.Pre, // Pre
sequence, // Sequence
match.Post, // Post
match.ModificationText, // Modifications
ion.Composition, // Composition
proteinName, // ProteinName
proteinDescription, // ProteinDescription
protLength, // ProteinLength
start, // Start position in protein
end, // End position in protein
ion.Charge, // precursorCharge
StringUtilities.DblToString(ion.GetMostAbundantIsotopeMz(), 9, true), // MostAbundantIsotopeMz
StringUtilities.DblToString(ion.Composition.Mass, 9, true), // Mass
match.NumMatchedFragments, // (Number of matched fragments)
StringUtilities.DblToString(probability, 4), // Probability
StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue), 6, true, 0.001), // EValue; will be displayed using scientific notation if the value is less than 0.001
StringUtilities.DblToString(ExcelMinValue(match.SpecEvalue * database.GetNumEntries()), 6, true, 0.001) // SpecEValue; will be displayed using scientific notation if the value is less than 0.001
);
}
}
}
public void CountMatchedScansPerProtein()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int minTagLength = 6;
var proteinToScan = new Dictionary<string, HashSet<int>>();
const string fastaFilePath = @"D:\Research\Data\CommonContaminants\H_sapiens_Uniprot_SPROT_2013-05-01_withContam.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);
Console.WriteLine(@"Sequence length: {0}", fastaDb.GetSequence().Length);
//const string tagFilePath = @"H:\Research\QCShew_TopDown\Production\QC_Shew_Intact_26Sep14_Bane_C2Column3_seqtag.tsv";
//const string tagFilePath = @"\\protoapps\UserData\Jungkap\Co_culture\23B_pellet_TD_3Feb14_Bane_PL011402.seqtag";
const string tagFilePath = @"D:\MassSpecFiles\co_culture\23A_pellet_TD_3Feb14_Bane_PL011402.seqtag";
if (!File.Exists(tagFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, tagFilePath);
}
var isHeader = true;
var numMatchedPairs = 0;
foreach (var line in File.ReadAllLines(tagFilePath))
{
if (isHeader)
{
isHeader = false;
continue;
}
var token = line.Split('\t');
if (token.Length != 3) continue;
var scan = Convert.ToInt32(token[0]);
var tag = token[1];
if (tag.Length < minTagLength) continue;
foreach (var matchedProtein in searchableDb.FindAllMatchedSequenceIndices(tag)
.Select(index => fastaDb.GetProteinName(index)))
{
++numMatchedPairs;
HashSet<int> matchedScans;
if (proteinToScan.TryGetValue(matchedProtein, out matchedScans))
{
matchedScans.Add(scan);
}
else
{
matchedScans = new HashSet<int> {scan};
proteinToScan.Add(matchedProtein, matchedScans);
}
}
}
var numMatchedProteins = proteinToScan.Keys.Count;
var numAllProteins = fastaDb.GetNumEntries();
Console.WriteLine("NumAllProteins: {0}", numAllProteins);
Console.WriteLine("NumMatchedProteins: {0}", numMatchedProteins);
Console.WriteLine("AvgMatchedScansPerProtein: {0}", numMatchedPairs / (float)numAllProteins);
}
public void TestFasta()
{
var db = new FastaDatabase(@"\\protoapps\UserData\Jungkap\Lewy\db\ID_005140_7A170668.fasta");
Console.WriteLine(db.GetNumEntries());
}
