private void buttonWork_Click(object sender, EventArgs e)
{
buttonWork.Text = "Busy!";
//First, lets get the input DB in RAM
PatternTools.FastaParser.FastaFileParser fp = new PatternTools.FastaParser.FastaFileParser();
fp.ParseFile(new StreamReader(textBoxInputFile.Text), false, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
if (checkBoxQualityFilters.Checked)
{
int itemsRemovedMinNo = fp.MyItems.RemoveAll(a => a.Sequence.Length <= (int)numericUpDownMinNoNT.Value);
labelNoNt.Text = itemsRemovedMinNo.ToString();
}
else
{
labelNoNt.Text = "0";
}
this.Update();
int itemsRemovedStopCoddons = 0;
StreamWriter sw = new StreamWriter(textBoxOutput.Text);
PatternTools.DNA2Protein translator = new PatternTools.DNA2Protein();
foreach (FastaItem fi in fp.MyItems)
{
List <string> translatedFrames = new List <string>();
if (radioButton3Frame.Checked)
{
translatedFrames = translator.Translate3(fi.Sequence);
}
else
{
translatedFrames = translator.Translate6(fi.Sequence);
}
for (int i = 0; i < translatedFrames.Count; i++)
{
if (checkBoxQualityFilters.Checked)
{
int noStopCodons = Regex.Matches(translatedFrames[i], Regex.Escape("*")).Count;
Console.WriteLine(fi.SequenceIdentifier + " Frame{0} StopCodons: {1}", i, noStopCodons);
if (noStopCodons >= (int)numericUpDownMaxNoStopCodons.Value)
{
itemsRemovedStopCoddons++;
labelNoStopCodons.Text = itemsRemovedStopCoddons.ToString();
this.Update();
}
}
else
{
sw.WriteLine(fi.SequenceIdentifier + "_" + i);
sw.WriteLine(translatedFrames[i]);
}
}
}
sw.Close();
Console.WriteLine("Done");
buttonWork.Text = "Go!";
}
static void Main(string[] args)
{
int minNoPeptides = 2;
double minAcceptableXCorr = 1.7;
string sequenceDB = @"C:\Users\pcarvalho\Desktop\XIC\BSA\PFUsmall.T-R";
string massSpectraFile = @"C:\Users\pcarvalho\Desktop\XIC\BSA\1\20111024_BSA_40fmol_01.RAW";
CometWrapper.cometParams cp = new CometWrapper.cometParams();
cp.ClearMZRangeMax = 0;
cp.ClearMZRangeMin = 0;
cp.Enzyme = 1; //Trypsin
cp.EnzymeSpecificity = 2;
cp.FragmentBinOffset = 0.4;
cp.FragmentBinTolerance = 1.0005;
cp.IonsA = false;
cp.IonsB = true;
cp.IonsC = false;
cp.IonsNL = true;
cp.IonsX = false;
cp.IonsY = true;
cp.IonsZ = false;
cp.MaxVariableModsPerPeptide = 3;
cp.MissedCleavages = 4;
Modification m1 = new Modification("Carb", (decimal)57.02146, "C");
//Modification m2 = new Modification("M", (decimal)15.9949, "M");
//m2.isDiff = true;
//For cross-linker dead end, include as a variable mod, and then as a variable mod for n-terminal
cp.MyModificationItems = new List <CometWrapper.Modification>()
{
m1
};
cp.PrecursorMassTolerance = 40;
cp.SearchMassRangeMax = 5500;
cp.SearchMassRangeMin = 550;
cp.SequenceDatabase = sequenceDB;
cp.TheoreticalFragIons = 1;
List <SQTScan2> myResults = CometWrapper.RemoteCall.CallComet(cp, massSpectraFile);
int removedPrimary = myResults.RemoveAll(a => a.Matches[0].PrimaryScore < minAcceptableXCorr);
var proteinIDs = (from result in myResults
from ID id in result.Matches[0].IDs
group id by id.Locus into myLocusGroups
select new { ID = myLocusGroups.Key, Count = myLocusGroups.Count() });
List <string> peptides = (from result in myResults
select result.Matches[0].PeptideSequence).Distinct().ToList();
PatternTools.FastaParser.FastaFileParser ffp = new PatternTools.FastaParser.FastaFileParser();
ffp.ParseFile(new StreamReader(cp.SequenceDatabase), true, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
List <FastaItem> myFasta = new List <FastaItem>();
foreach (var prot in proteinIDs)
{
if (prot.Count >= minNoPeptides)
{
myFasta.Add(ffp.MyItems.Find(a => a.SequenceIdentifier.Equals(prot.ID)));
}
}
Console.WriteLine("Done");
}
private void DoJob()
{
try
{
PatternTools.FastaParser.FastaFileParser fp = new PatternTools.FastaParser.FastaFileParser();
buttonGoText = "Working!";
statusBarText = "Parsing DB...";
backgroundWorker1.ReportProgress(1);
Regex myRegex = new Regex(textBoxNameRegex.Text, RegexOptions.Compiled);
PatternTools.FastaParser.DBTypes dbType;
if (radioButtonDBNCBI.Checked)
{
dbType = DBTypes.NCBInr;
}
else if (radioButtonDBUniprot.Checked)
{
dbType = DBTypes.UniProt;
}
else if (radioButtonDBGeneric.Checked)
{
dbType = DBTypes.IDSpaceDescription;
}
else if (radioButtonNextProt.Checked)
{
dbType = DBTypes.NeXtProt;
}
else
{
dbType = PatternTools.FastaParser.DBTypes.IPI;
}
if (includeContaminants)
{
byte[] byteArray = Encoding.ASCII.GetBytes(NCBIExtractor.Properties.Resources.ContaminantDB);
StreamReader sContaminantsr = new StreamReader(new MemoryStream(byteArray));
fp.ParseFile(
sContaminantsr,
false,
PatternTools.FastaParser.DBTypes.Contaminant);
}
foreach (DataGridViewRow r in dataGridViewInputDBs.Rows)
{
PatternTools.FastaParser.FastaFileParser fpTmp = new PatternTools.FastaParser.FastaFileParser();
string fileName = r.Cells[0].Value.ToString();
StreamReader srDB = new StreamReader(fileName);
fpTmp.ParseFile(
srDB,
false,
dbType,
true,
new Regex(textBoxNameRegex.Text, RegexOptions.IgnoreCase));
srDB.Close();
fpTmp.MyItems.RemoveAll(a => string.IsNullOrEmpty(a.Sequence));
fp.MyItems.AddRange(fpTmp.MyItems);
}
if (removeSubSequences)
{
if (numericUpDownIdentity.Value == 100)
{
Console.WriteLine("Removing subset sequences");
List <FastaItem> toEliminate = new List <FastaItem>();
Console.WriteLine("Searching for subset sequences...");
//order by increasing length
fp.MyItems.Sort((a, b) => a.Sequence.Length.CompareTo(b.Sequence.Length));
for (int i = 0; i < fp.MyItems.Count; i++)
{
Console.WriteLine("Analyzing for sequence " + i);
for (int j = i + 1; i < fp.MyItems.Count; j++)
{
if (j == fp.MyItems.Count)
{
break;
}
if (fp.MyItems[j].Sequence.Contains(fp.MyItems[i].Sequence))
{
toEliminate.Add(fp.MyItems[i]);
Console.WriteLine("subset sequence found");
fp.MyItems[j].Description = fp.MyItems[j].Description + " : " + fp.MyItems[i].SequenceIdentifier + " " + fp.MyItems[i].Description;
break;
}
}
}
Console.WriteLine("Sequences eliminated: " + toEliminate.Count);
fp.MyItems = fp.MyItems.Except(toEliminate).ToList();
}
else
{
MAligner.MCompress.Compress c = new MAligner.MCompress.Compress();
c.CompressByIdentity(fp, (double)numericUpDownIdentity.Value / 100.0, null);
}
}
statusBarText = "Writing DB...";
backgroundWorker1.ReportProgress(1);
fp.GenerateSearchDB(outputFile, includeReversed, includeScrambled0, includeScrambled1, radioButtonTPRMR.Checked);
myFileParserItems = fp.MyItems.Count();
}
catch (Exception ee)
{
MessageBox.Show(ee.Message);
}
}
