static public void ConvertFasta()
{
int counter = 0;
string line;
string sFile = @"data\Homo_sapiens.GRCh37.hg19.dna.chromosome.4.fa";
String sFileNew = @"data\chr4.hg19.fac";
FastaConverter fastaConverter = new FastaConverter(App.Path + sFile);
bool b = fastaConverter.Convert(App.Path + sFileNew);
if (b)
{
App.Log("Conversion to " + sFileNew + " was successful");
}
else
{
App.Log("Conversion failed");
}
// Read the file and display it line by line.
StreamReader file = new StreamReader(App.Path + sFile);
App.Log("Opening " + sFile);
while ((line = file.ReadLine()) != null)
{
App.Log(line);
counter++;
if (counter > 30)
{
break;
}
}
file.Close();
}
static public String FusionHmmScan(String title, String seq1, String seq2)
{
String ret = "";
seq1 = FastaConverter.ConvertString(seq1);
seq2 = FastaConverter.ConvertString(seq2);
List <String> seqs = new List <string>();
for (int i = 0; i < 5; i++)
{
seqs.Add(seq1 + seq2); // + +
seqs.Add(seq1 + Sequencer.InvCompl(seq2)); // + -
seqs.Add(Sequencer.InvCompl(seq1) + seq2); // - +
// 20% deletieren
int cut1 = (int)Math.Round(seq1.Length * 0.2);
int cut2 = (int)Math.Round(seq2.Length * 0.2);
seq1 = seq1.Substring(0, seq1.Length - cut1);
seq2 = seq2.Substring(cut2);
}
List <String> orfs = new List <string>();
foreach (String seq in seqs) // 6-frame ORFs
{
orfs.Add(seq.Substring(0));
orfs.Add(seq.Substring(1));
orfs.Add(seq.Substring(2));
String seqInv = Sequencer.InvCompl(seq);
orfs.Add(seqInv.Substring(0));
orfs.Add(seqInv.Substring(1));
orfs.Add(seqInv.Substring(2));
}
Hmmer hmmer = new Hmmer();
Hmmer.SetDatabase("PFam-A");
Hmmer.Debug = true;
int c = 0;
foreach (String orf in orfs)
{
String peptide = Sequencer.Translate(orf, true); // Translatieren ohne Stop-Codon
hmmer.AddSequence(peptide, title + " #" + c.ToString());
c++;
}
hmmer.DoScan();
List <Hmmer.Result> results = hmmer.GetResults();
List <string> resultsUnique = new List <string>();
ret += "> " + title + Environment.NewLine;
foreach (Hmmer.Result result in results)
{
if (result.Evalue >= 1)
{
continue;
}
string res = result.Accession + ": " + result.Name;
if (!resultsUnique.Contains(res))
{
resultsUnique.Add(res);
ret += res + Environment.NewLine;
}
}
ret += Environment.NewLine;
return(ret);
}
