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);
}
protected void OnFusionEvent(Range fragment1, Range fragment2)
{
Exon ex1 = Source.WithinExon(fragment1.End);
Exon ex2 = Source.WithinExon(fragment2.Start);
// 10371808
// 103718617
if ((ex1 != null) && (ex2 != null))
{
// Both sides of the cut are within exons
if (ex1.Strand == ex2.Strand)
{
// Both exons are on same strand
int bpExon1 = (int)(fragment1.End - ex1.Start);
int bpExon2 = (int)(ex2.End - fragment2.Start);
int percentExon1 = (int)(((double)bpExon1 / ex1.Length) * 100);
int percentExon2 = (int)(((double)bpExon2 / ex2.Length) * 100);
if ((bpExon1 > 100) && (bpExon2 > 100))
{
String seqFusion, seq1, seq2;
Range rangeLeft = new Range(ex1.Start, fragment1.End);
Range rangeRight = new Range(fragment2.Start, ex2.End);
seq1 = Source.Read(rangeLeft.Start, (int)rangeLeft.Length);
seq2 = Source.Read(rangeRight.Start, (int)rangeRight.Length);
seqFusion = seq1 + seq2;
Dictionary <String, String> orfs = new Dictionary <string, string>();
orfs.Add("Forward 0", Sequencer.GetORF(seqFusion, 0));
orfs.Add("Forward 1", Sequencer.GetORF(seqFusion, 1));
orfs.Add("Forward 2", Sequencer.GetORF(seqFusion, 2));
String seqInv = Sequencer.Invert(Sequencer.Complement(seqFusion));
orfs.Add("Reverse 0", Sequencer.GetORF(seqInv, 0));
orfs.Add("Reverse 1", Sequencer.GetORF(seqInv, 1));
orfs.Add("Reverse 2", Sequencer.GetORF(seqInv, 2));
Dictionary <String, String> peptides = new Dictionary <string, string>();
bool bSignificantPeptides = false;
foreach (String key in orfs.Keys)
{
if (orfs[key].Length >= 120)
{
String pep = Sequencer.Translate(orfs[key]);
peptides.Add(key, pep);
bSignificantPeptides = true;
}
}
if (bSignificantPeptides)
{
NumGenes++;
String htmlEx1 = "<a href='http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=1;q=" + ex1.Name +
"' target='_blank'>" + ex1.Name + "</a> " + bpExon1.ToString() + "bp (" + percentExon1.ToString() + "%)";
String htmlEx2 = "<a href='http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=1;q=" + ex2.Name +
"' target='_blank'>" + ex2.Name + "</a> " + bpExon2.ToString() + "bp (" + percentExon2.ToString() + "%)";
if (ExtendedOutput)
{
App.Log("<b>Found Fusion Gene #" + NumGenes + ": </b>" + htmlEx1 + " <b>&</b> " + htmlEx2 + "");
}
// App.Log("Fusion Sequence: " + seqFusion);
foreach (String key in peptides.Keys)
{
String pep = peptides[key];
if (ExtendedOutput)
{
App.Log(key + ": " + pep);
}
FusionSequence fs = new FusionSequence();
fs.SequenceId = NumOrf.ToString();
fs.IsHit = false;
fs.Exon1 = ex1;
fs.Exon2 = ex2;
fs.OrfName = key;
fs.Range1 = rangeLeft;
fs.Range2 = rangeRight;
fs.Sequence = pep;
FusionSequences.Insert(NumOrf, fs);
Hmmer.AddSequence(pep, fs.SequenceId);
//String sequenceName = "#" + NumGenes+" "+ex1.Name + " " + percentExon1.ToString() + "% & " + ex2.Name + " " + percentExon2.ToString() + "% ORF " + key;
NumOrf++;
}
} // if (bSignificantPeptides)
} // if ((bpExon1 > 100) && (bpExon2 > 100))
} // if (ex1.Strand == ex2.Strand)
} // if ((ex1 != null) && (ex2 != null))
else
{
//App.Log("No Fusion Gene :(");
}
}
