public static List <UniProtOrGenePeptItem> ParseUniprotFile(string fileName)
{
StreamReader sr = new StreamReader(fileName);
string line;
List <UniProtOrGenePeptItem> myUniprotItems = new List <UniProtOrGenePeptItem>();
UniProtOrGenePeptItem u = new UniProtOrGenePeptItem(new List <string>());
int counter = 0;
while ((line = sr.ReadLine()) != null)
{
counter++;
try
{
if (line.StartsWith("AC "))
{
string[] cols = Regex.Split(line, " ");
string[] terms = Regex.Split(cols[1], ";");
myUniprotItems.Add(u);
u = new UniProtOrGenePeptItem(terms.ToList());
}
if (line.StartsWith("DR "))
{
string[] cols = Regex.Split(line, ";");
foreach (string s in cols)
{
if (s.StartsWith(" GO:"))
{
string corrected = Regex.Replace(s, " GO:", "");
u.GOItems.Add(corrected);
}
}
}
}
catch
{
Console.WriteLine("Error parsing line " + counter);
}
}
myUniprotItems.Add(u);
return(myUniprotItems);
}
public static List <UniProtOrGenePeptItem> ParseGenePeptFile(string fileName)
{
StreamReader sr = new StreamReader(fileName);
string line;
List <UniProtOrGenePeptItem> myUniprotItems = new List <UniProtOrGenePeptItem>();
UniProtOrGenePeptItem u = null;
int counter = 0;
Regex goCapture = new Regex("GO:([0-9]{3,})");
while ((line = sr.ReadLine()) != null)
{
counter++;
if (line.StartsWith("VERSION "))
{
List <string> cols = Regex.Split(line, " ").ToList();
List <string> terms = Regex.Split(cols.Last(), ";").ToList();
for (int i = 0; i < terms.Count; i++)
{
terms[i] = terms[i].Replace("GI:", "");
}
u = new UniProtOrGenePeptItem(terms);
myUniprotItems.Add(u);
}
if (line.Contains("GO:"))
{
foreach (Match m in goCapture.Matches(line))
{
string mtmp = m.ToString();
mtmp = mtmp.Substring(3, mtmp.Length - 3);
myUniprotItems.Last().GOItems.Add(mtmp);
}
}
}
myUniprotItems.Add(u);
myUniprotItems.RemoveAll(a => a.GOItems.Count == 0);
return(myUniprotItems);
}
