public static void AddFastaToArcog(FastaObj fasta, ArCOGObj arcog)
{
List<FastaObj> fastaList;
if (!Program.activeArCOGFastaClasses.TryGetValue(arcog, out fastaList))
{
fastaList = new List<FastaObj>();
Program.activeArCOGFastaClasses.Add(arcog, fastaList);
}
fastaList.Add(fasta);
}
public BlastEntry(string header, string info)
{
this.rawHeader = header;
this.rawInfo = info;
var index = info.IndexOf("Score");
var endIndex = info.IndexOf(",", index);
var ss1 = info.Substring(index, endIndex - index).Replace(" ", "");
var ts1 = ss1.IndexOf('=') + 1;
var scoreSTR = ss1.Substring(ts1, ss1.IndexOf('b') - ts1);
var score = Convert.ToDouble(scoreSTR);
index = info.IndexOf("Expect");
endIndex = info.IndexOf(",", index);
ss1 = info.Substring(index, endIndex - index).Replace(" ", "");
ts1 = ss1.IndexOf('=') + 1;
var evalueSTR = ss1.Substring(ts1, ss1.Length - ts1);
var eindex = evalueSTR.IndexOf('e');
var evalue = 0.0;
if (eindex != -1)
{
var v1 = evalueSTR.Substring(0, eindex);
var v2 = evalueSTR.Substring(eindex + 1);
evalue = Convert.ToDouble(v1) * Math.Pow(10, Convert.ToDouble(v2));
}
else
{
evalue = Convert.ToDouble(evalueSTR);
}
index = info.IndexOf("Identities");
endIndex = info.IndexOf(",", index);
ss1 = info.Substring(index, endIndex - index).Replace(" ", "");
ts1 = ss1.IndexOf('(') + 1;
var identity = Convert.ToDouble(ss1.Substring(ts1, ss1.IndexOf("%") - ts1)) / 100.0;
this.blastFasta = new FastaObj(header, null);
this.Score = score;
this.EValue = evalue;
this.Identity = identity;
return;
}
public BlastObj(string queryPath, string blastTextPath)
{
var qTxt = Management.GetTextFromFile(queryPath);
var bTxt = Management.GetTextFromFile(blastTextPath);
this.queryFasta = new FastaObj(qTxt[0], qTxt[1]);
var btxtL = bTxt.ToList<String>();
var changed = false;
for (int i = 0; i < btxtL.Count; i++)
{
var cnt = 0;
var ns = new List<String>();
for (int j = 0; j < btxtL[i].Length; j++)
{
if (btxtL[i][j] == '>')
{
cnt++;
if (cnt == 1)
continue;
changed = true;
ns.Add(btxtL[i].Substring(0, j));
btxtL[i] = btxtL[i].Substring(j);
j = 0;
}
continue;
}
while (ns.Count > 0)
{
btxtL.Insert(i + 1, ns[0]);
ns.RemoveAt(0);
}
}
if (changed)
bTxt = btxtL.ToArray<string>();
int curRowIndex = 0;
while (curRowIndex < bTxt.Length)
{
int startIndex = bTxt[curRowIndex].IndexOf(@">", 0);
if (startIndex == -1)
{
curRowIndex++;
continue;
}
int i = 1, headerEndIndex = -1, fastaEndIndex = -1;
for (i = 1; i + curRowIndex <= bTxt.Length; i++)
{
if ((headerEndIndex != -1 && fastaEndIndex != -1))
break;
if (i + curRowIndex >= bTxt.Length)
{
if (headerEndIndex != -1 && fastaEndIndex == -1)
fastaEndIndex = i + curRowIndex - 1;
break;
}
if (headerEndIndex == -1 && bTxt[i + curRowIndex].Contains("]"))
headerEndIndex = i + curRowIndex;
if (fastaEndIndex == -1 && headerEndIndex != -1 && bTxt[i + curRowIndex].Contains(">"))
fastaEndIndex = (i - 1) + curRowIndex;
continue;
}
if (headerEndIndex == -1 || fastaEndIndex == -1)
break;
var header = "";
var fastaInfo = "";
for (i = curRowIndex; i <= headerEndIndex; i++)
if (bTxt[i].Contains('>'))
header += bTxt[i].Substring(bTxt[i].IndexOf(">"));
else
header += bTxt[i];
for (i = headerEndIndex + 1; i <= fastaEndIndex; i++)
fastaInfo += bTxt[i];
var hei = header.IndexOf("Length=");
if (hei != -1 && hei + 1 < header.Length)
{
fastaInfo = header.Substring(hei) + fastaInfo;
header = header.Substring(0, hei);
}
var be = new BlastEntry(header, fastaInfo);
this.entries.Add(be);
curRowIndex++;
continue;
}
/*
var x = 0;
var ids = new List<int>();
foreach (String s in bTxt)
foreach (Char c in s)
{
if (c == '>')
{
x++;
var ind = s.IndexOf("|", 5);
var ts = s.Substring(5, ind - 5);
ids.Add(Convert.ToInt32(ts));
}
}
var ids2 = new List<int>();
foreach (BlastEntry be in this.entries)
ids2.Add(be.fastaInfo.giID);
foreach(int id in ids)
if (!ids2.Contains(id))
{
continue;
}*/
return;
}