public Exon(Exon e)
{
chromosome = e.chromosome;
Id = e.Id;
Range = e.Range;
Strand = e.Strand;
Name = e.Name;
}
public static void TestNullModell4(String nameNull)
{
Chromosome chrOrig = new Chromosome("4");
Chromosome chrNull = new Chromosome(nameNull);
int idOrig = chrOrig.Id;
int idNull = chrNull.Id;
Range rangeOrig = chrOrig.GetQ();
System.Data.Common.DbDataReader res =
App.DB.Query("SELECT * FROM exon WHERE chromosomeId=" + idOrig + " AND start >= " +
rangeOrig.Start + " AND end <= " + rangeOrig.End + " ORDER BY start asc");
/*
* App.DB.Query("SELECT * FROM exon WHERE chromosomeId=" + idOrig + " AND start >= " +
* rangeOrig.Start + " AND end <= " + rangeOrig.End + " ORDER BY RANDOM() LIMIT 50");
* */
int i = 0;
while (res.Read())
{
String name = res["name"].ToString();
Exon exonOrig = new Exon(res, chrOrig);
System.Data.Common.DbDataReader resNull = App.DB.QueryRead("SELECT * FROM exon WHERE name='" +
name + "' AND chromosomeId=" + idNull);
if (!resNull.HasRows)
{
App.Log(name + " not found in " + nameNull);
continue;
}
Exon exonNull = new Exon(resNull, chrNull);
String seqOrig = exonOrig.Read();
String seqNull = exonNull.Read();
if (seqOrig == seqNull)
{
// if (exonNull.Strand != exonOrig.Strand) App.Log("Strand switcher! :");
App.Log("#" + i + " " + name + " OK");
}
else
{
App.Log("#" + i + " " + name + " FFFFFUUUUUUU....");
}
i++;
}
}
private void LoadExons()
{
Exons = new Exon[0];
List <Exon> list = new List <Exon>();
App.Status("Loading exons. This may take a while...");
System.Data.Common.DbDataReader res =
App.DB.Query("SELECT * FROM exon WHERE chromosomeId=" + Id + " ORDER BY start ASC");
App.Status("Saving exons.");
while (res.Read())
{
Exon exon = new Exon(res, this);
list.Add(exon);
}
Exons = list.ToArray();
App.Status("Indexing exons.");
int numIndizes = (int)(Length / ExonRangeSize);
ExonStarts = new int[numIndizes];
int exonStart = 0;
for (int i = 0; i < numIndizes; i++)
{
int start = i * ExonRangeSize;
for (int j = exonStart; j < Exons.Length; j++)
{
if (Exons[j].Start >= start)
{
ExonStarts[i] = j;
exonStart = j;
break;
}
}
}
App.Status();
LoadedExons = true;
}
private void CreateChromosome()
{
App.DB.OpenFast();
SQLiteCommand command = App.DB.CreateCommand();
SQLiteTransaction transaction = App.DB.BeginTransaction();
command.Transaction = transaction;
String sql = "INSERT INTO exon (exonId, name, geneId, start, end, strand, isVirtual, chromosomeId) " +
"VALUES(@exonId, @name, @geneId, @start, @end, @strand, 1, " + NewChromosomeId + ")";
command.CommandText = sql;
int posOld = SourceRange.Start;
int posNew = 1;
int curGene = 0;
byte[] buffer;
FileStream fNew = File.Create(NewFilePath);
do
{
App.Status("Writing Gene " + (curGene + 1) + " of " + Genes.Count);
Gene geneOld = null;
Gene geneNew = null;
// WriteNonCodingSequence
int nonCodingLength = 0;
if (curGene < Genes.Count)
{
geneOld = Genes[curGene];
geneNew = Genes[PositionsShuffled[curGene]];
nonCodingLength = geneOld.Start - posOld;
if (nonCodingLength < 0)
{
/* App.Log("Overlapping Gene: " + geneOld.Name + " - skipping");
* curGene++;
* continue;*/
int diff = posOld - geneOld.Start;
App.Log("Overlapping Gene: " + geneOld.Name + " - " + diff + "bp");
posOld = geneOld.Start;
nonCodingLength = 0;
}
}
else
{
nonCodingLength = SourceRange.End - posOld;
}
if (nonCodingLength > 0)
{
Source.ReadBuffer(posOld, nonCodingLength, out buffer);
// App.Log("Reading Non Coding Sequence from pos " + posOld + ", length " + nonCodingLength);
fNew.Write(buffer, 0, buffer.Length);
}
posOld += nonCodingLength;
posNew += nonCodingLength;
// App.Log("# " + curGene + " NC Length " + nonCodingLength);
if (curGene >= Genes.Count)
{
break;
}
bool switchStrand = App.Random.NextBool();
// switchStrand = false;
// WriteNewGene
Source.ReadBuffer(geneNew.Start, geneNew.Length, out buffer);
//App.Log("Reading Gene New from pos " + geneNew.Start + ", length " + geneNew.Length);
Gene geneNewNull = new Gene(geneNew);
geneNewNull.Range = new Range(posNew, posNew + geneNew.Length);
if (switchStrand)
{
Sequencer.InvCompl(ref buffer);
if (geneNewNull.Strand == 1)
{
geneNewNull.Strand = -1;
}
else
{
geneNewNull.Strand = 1;
}
// App.Log("Switched Strands");
}
fNew.Write(buffer, 0, buffer.Length);
// Exons
System.Data.Common.DbDataReader res =
App.DB.Query("SELECT * FROM exon WHERE geneId=" + geneNew.Id + " and chromosomeId = " + Source.Id + " ORDER BY start ASC");
while (res.Read())
{
Exon exonOld = new Exon(res, Source);
Exon exonNew = new Exon(exonOld);
int bpFromGeneStart = exonNew.Start - geneNew.Start;
int newStart = geneNewNull.Start + bpFromGeneStart;
int newEnd = newStart + exonOld.Length;
if (switchStrand)
{
newStart = geneNewNull.End - bpFromGeneStart - exonOld.Length;
newEnd = geneNewNull.End - bpFromGeneStart;
}
exonNew.Range = new Range(newStart, newEnd);
exonNew.Strand = geneNewNull.Strand;
command.Parameters.AddWithValue("@exonId", exonNew.Id);
command.Parameters.AddWithValue("@geneId", geneNewNull.Id);
command.Parameters.AddWithValue("@start", newStart);
command.Parameters.AddWithValue("@end", newEnd);
command.Parameters.AddWithValue("@strand", exonNew.Strand);
command.Parameters.AddWithValue("@name", exonNew.Name);
command.ExecuteNonQuery();
}
App.Log("# " + curGene + " " + geneNewNull.Name + "(ID " + geneNewNull.Id + ") -> " + geneOld.Name + " - Pos: " + geneNewNull.Start + " Strand: " + geneOld.Strand + (switchStrand ? " (reversed)" : ""));
// App.Log("# " + curGene + " New Gene Length " + geneNew.Length);
// App.Log("# " + curGene + " posNew " + posNew + " - posOld "+posOld);
// App.Log("# " + curGene + " Old Gene Distance " + (Genes[curGene+1].Start-geneOld.Start));
// Next Gene
long filePos = fNew.Position;
posNew += geneNewNull.Length;
posOld += geneOld.Length;
App.Assert(filePos == (posNew - 1));
curGene++;
App.LogScroll();
// if (curGene > 40) break;
}while (posOld <= SourceRange.End);
fNew.Close();
transaction.Commit();
command.Dispose();
App.DB.Exec("UPDATE chromosome SET length=" + posNew + " WHERE id=" + NewChromosomeId);
App.DB.Close();
App.Status("");
}
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 :(");
}
}