//----------------------------------------------------------
private void Parse(AssociationType t)
{
if (t.Equals(AssociationType.UniProt))
{
string line = "";
StreamReader sr = new StreamReader(GOAfileName);
associationDic.Clear();
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("Uni"))
{
continue;
}
string[] cols = Regex.Split(line, "\t");
string GoID = Regex.Replace(cols[4], "GO:", "");
string vs = cols[10];
string[] UniprotIDs = Regex.Split(vs, Regex.Escape("|"));
foreach (string u in UniprotIDs)
{
string theString = u;
if (u.Contains("_"))
{
string[] cols2 = Regex.Split(u, "_");
theString = cols2[0];
}
if (associationDic.ContainsKey(theString))
{
if (!associationDic[theString].Contains(GoID))
{
associationDic[theString].Add(GoID);
}
}
else
{
associationDic.Add(theString, new List <string>()
{
GoID
});
}
}
}
}
else
{
string read;
Regex tabSpliter = new Regex(@"\t");
Regex semiColenSpliter = new Regex(@";");
Regex PipeSpliter = new Regex(@"\|");
StreamReader sr = new StreamReader(GOAfileName);
int conversionIndex = 10; //The column where the IPI's are located
int theGOColumn = 4; // The GO Column for the IPI database
if (t.Equals(AssociationType.Generic))
{
conversionIndex = myColumn;
theGOColumn = GOColumn;
}
while ((read = sr.ReadLine()) != null)
{
if (read.StartsWith("!") || read.Length == 0)
{
continue;
}
string[] ids = tabSpliter.Split(read);
//Modification here
//The IPIs column 10, //GOs column 4 //PlasmoDraft column 1
ids[theGOColumn] = System.Text.RegularExpressions.Regex.Replace(ids[theGOColumn], "GO:", "");
//First, lets extract the IPIs
string[] IDsInRow = PipeSpliter.Split(ids[conversionIndex]);
List <string> IPIs = new List <string>();
foreach (string s in IDsInRow)
{
if (s.Contains("IPI"))
{
IPIs.Add(s);
}
if (t.Equals(AssociationType.Generic))
{
IPIs.Add(s);
}
}
foreach (string IPI in IPIs)
{
if (associationDic.ContainsKey(IPI))
{
//We should only add the GO Term if it is not in the array;
if (!associationDic[IPI].Contains(ids[theGOColumn]))
{
associationDic[IPI].Add(ids[theGOColumn]);
}
}
else
{
List <string> theList = new List <string>();
theList.Add(ids[theGOColumn]);
associationDic.Add(IPI, theList);
}
}
}
sr.Close();
}
}
