public static DigestedFastaFile performDigest(FastaFile f, int numMissedCleavages)
{
// The input fasta file path
String fastaFilePath = f.getFileName();
return(performDigest(fastaFilePath, numMissedCleavages, true));
}
private static Database databaseSetUp(String fasta_file_name)
{
FastaFile f = Loader.parseFasta(fasta_file_name);
DigestedFastaFile df = PerformDigestion.performDigest(f, GlobalVar.NUM_MISSED_CLEAVAGES);
int numberOfProteinsInFasta = f.getAccessionToFullSequence().Count;
int numberOfPeptidesInDigestedFasta = df.getDigestedPeptideArray().Count;
log.Info("Fasta file: " + fasta_file_name);
log.Info("Num missed cleavages: " + GlobalVar.NUM_MISSED_CLEAVAGES);
log.Info("Number of proteins: " + numberOfProteinsInFasta);
log.Info("Number of peptides: " + numberOfPeptidesInDigestedFasta);
log.Debug("Constructing graph...");
Database g;
if (GlobalVar.isSimulationForFeatureExtraction == true)
{
g = new Database(f, df, true, false);
}
else
{
g = new Database(f, df, true, true);
}
log.Debug(g);
return(g);
}
public static DigestedFastaFile performDigest(Dictionary <String, Protein> protein_hash, int numMissedCleavages)
{
String tempOutput = "temp.tsv";
Writer.writeFastaFile(tempOutput, new List <Protein>(protein_hash.Values));
FastaFile f = new FastaFile(tempOutput, protein_hash);
return(performDigest(f, numMissedCleavages));
}
private void btnReadFasta_Click(object sender, EventArgs e)
{
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
List<Protease.Type> ProteaseType = new List<Protease.Type>();
if (chkEnzy_Trypsin.Checked)//Trypsin
{
ProteaseType.Add(Protease.Type.Trypsin);
}
if (chkEnzy_GlucE.Checked)//GlucE
{
ProteaseType.Add(Protease.Type.GlucE);
}
if (chkEnzy_GlucED.Checked) //GlucED
{
ProteaseType.Add(Protease.Type.GlucED);
}
if (chkEnzy_None.Checked || ProteaseType.Count == 0)
{
ProteaseType.Add(Protease.Type.None);
}
enumPeptideMutation pepMuta = enumPeptideMutation.NoMutation;
if (cboPepMutation.SelectedIndex == 1)
{
pepMuta = enumPeptideMutation.DtoN;
}
else if (cboPepMutation.SelectedIndex == 2)
{
pepMuta = enumPeptideMutation.AnyToN;
}
string fastaFile = openFileDialog1.FileName;
FastaFile file = new FastaFile(fastaFile);
List<string> Peptides = file.CreateCleavedPeptides(Convert.ToInt32(txtMissCleavage.Text), ProteaseType);
txtPeptides.Text = "Digested Peptides" + Environment.NewLine + Environment.NewLine;
foreach (string p in Peptides)
{
txtPeptides.Text += p + Environment.NewLine;
}
txtPeptides.Text += Environment.NewLine + Environment.NewLine + Environment.NewLine + Environment.NewLine;
txtPeptides.Text += "N-linked Peptides" + Environment.NewLine + Environment.NewLine;
List<string> lstPeptides = file.CreateCleavedNGlycoPeptides(Convert.ToInt32(txtMissCleavage.Text), ProteaseType, pepMuta);
foreach (string p in lstPeptides)
{
txtPeptides.Text += p + Environment.NewLine;
}
}
}
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification,
bool _includeRetentionTime, double _retentionTimeWindow)
{
includeCarbamidoModification = _includeCarbamidoModification;
includeRetentionTime = _includeRetentionTime;
retentionTimeWindow = _retentionTimeWindow;
log.Debug("Constructing graph...");
SequenceToPeptide = new Dictionary <String, Peptide>();
peptides = new List <Peptide>();
AccesstionToProtein = fastaFile.getAccessionToFullSequence();
addPeptides(digestedFastaFile.getDigestedPeptideArray());
log.Debug("Done constructing graph.");
}
public static Database loadExclusionDatabase(FastaFile fasta, DigestedFastaFile digestedFasta)
{
return(new Database(fasta, digestedFasta));
}
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification,
bool _includeRetentionTime) : this(fastaFile, digestedFastaFile, _includeCarbamidoModification, _includeRetentionTime,
DEFAULT_RETENTION_TIME_WINDOW)
{
}
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile) :
this(fastaFile, digestedFastaFile, DEFAULT_INCLUDE_CARBAMIDO_MODIFICATION, DEFAULT_INCLUDE_RETENTION_TIME)
{
}
