public static Dictionary <string, MiniProteinAnnotation> ReadMapping(string filename, HashSet <string> allProtIds)
{
StreamReader reader = FileUtils.GetReader(filename);
Dictionary <string, MiniProteinAnnotation> result = new Dictionary <string, MiniProteinAnnotation>();
string header = reader.ReadLine();
string[] h = header.Split('\t');
Dictionary <int, FeatureType> upMap = new Dictionary <int, FeatureType>();
for (int i = 6; i < h.Length; i++)
{
string q = h[i];
if (q.StartsWith("UniprotFeature:"))
{
string name = q.Substring(q.IndexOf(':') + 1);
upMap.Add(i, FeatureType.GetFeatureType(name));
}
}
string line;
while ((line = reader.ReadLine()) != null)
{
string[] a = line.Split('\t');
if (a.Length < 8)
{
continue;
}
Dictionary <FeatureType, List <UniprotFeature> > flist = new Dictionary <FeatureType, List <UniprotFeature> >();
string[] accessions = a[0].Length == 0 ? new string[0] : a[0].Split(';');
string geneName = a[1];
string proteinName = a[2];
string[] pfams = a[3].Length == 0 ? new string[0] : a[3].Split(';');
string[] pdbs = a[4].Length == 0 ? new string[0] : a[4].Split(';');
bool isReviewed = a[5].Equals("T");
for (int i = 6; i < a.Length; i++)
{
string u = a[i];
if (u.Length > 0)
{
FeatureType ft = upMap[i];
if (!flist.ContainsKey(ft))
{
flist.Add(ft, new List <UniprotFeature>());
}
string[] w = u.Split(';');
foreach (string s in w)
{
string[] u1 = s.Split(',');
if (u1.Length > 4)
{
flist[ft].Add(new UniprotFeature(u1));
}
}
}
}
MiniProteinAnnotation mpa = new MiniProteinAnnotation(geneName, proteinName, pfams, pdbs, isReviewed, flist);
foreach (string key in accessions)
{
if (!allProtIds.Contains(key))
{
continue;
}
if (!result.ContainsKey(key))
{
result.Add(key, mpa);
}
}
}
reader.Close();
return(result);
}
public static Dictionary<string, MiniProteinAnnotation> ReadMapping(string filename, HashSet<string> allProtIds)
{
StreamReader reader = FileUtils.GetReader(filename);
Dictionary<string, MiniProteinAnnotation> result = new Dictionary<string, MiniProteinAnnotation>();
string header = reader.ReadLine();
string[] h = header.Split('\t');
Dictionary<int, FeatureType> upMap = new Dictionary<int, FeatureType>();
for (int i = 6; i < h.Length; i++){
string q = h[i];
if (q.StartsWith("UniprotFeature:")){
string name = q.Substring(q.IndexOf(':') + 1);
upMap.Add(i, FeatureType.GetFeatureType(name));
}
}
string line;
while ((line = reader.ReadLine()) != null){
string[] a = line.Split('\t');
if (a.Length < 8){
continue;
}
Dictionary<FeatureType, List<UniprotFeature>> flist = new Dictionary<FeatureType, List<UniprotFeature>>();
string[] accessions = a[0].Length == 0 ? new string[0] : a[0].Split(';');
string geneName = a[1];
string proteinName = a[2];
string[] pfams = a[3].Length == 0 ? new string[0] : a[3].Split(';');
string[] pdbs = a[4].Length == 0 ? new string[0] : a[4].Split(';');
bool isReviewed = a[5].Equals("T");
for (int i = 6; i < a.Length; i++){
string u = a[i];
if (u.Length > 0){
FeatureType ft = upMap[i];
if (!flist.ContainsKey(ft)){
flist.Add(ft, new List<UniprotFeature>());
}
string[] w = u.Split(';');
foreach (string s in w){
string[] u1 = s.Split(',');
if (u1.Length > 4){
flist[ft].Add(new UniprotFeature(u1));
}
}
}
}
MiniProteinAnnotation mpa = new MiniProteinAnnotation(geneName, proteinName, pfams, pdbs, isReviewed, flist);
foreach (string key in accessions){
if (!allProtIds.Contains(key)){
continue;
}
if (!result.ContainsKey(key)){
result.Add(key, mpa);
}
}
}
reader.Close();
return result;
}
