static void Main(string[] args)
{
Peptide peptideList = new Peptide();
List<string> peptideSeqList = new List<string>();
string file = "C:\\Users\\Dong\\Desktop\\test.pep.list";
TextReader tr = new StreamReader(file);
string line;
while ((line = tr.ReadLine()) != null)
{
string peptide;
if (line.Contains("."))
{
string[] strs = line.Split('.');
peptide = strs[1];
}
else
peptide = line;
peptideSeqList.Add(peptide);
}
//remove duplicates of the peptides
//make it a unique list
peptideSeqList = removeDuplicate(peptideSeqList);
//generate the peptide list
//by putting the peptide
foreach (var pep in peptideSeqList)
{
//something wrong here!!!
peptideList.Add(1, "");
}
//Pep2Pro pp = new Pep2Pro();
string database = "C:\\Users\\Dong\\Desktop\\yates.fasta";
ProteomeDataFile foo = new ProteomeDataFile(database);
pwiz.CLI.proteome.ProteinList proteinList = foo.proteinList;
List<Protein> finalProteinList = new List<Protein>();
for (int i = 0; i < proteinList.size(); i++)
{
Protein protein = proteinList.protein(i, true);
if (!protein.id.Contains("Reverse"))
{
string sequence = protein.sequence;
//Console.WriteLine(protein.index);
foreach (var pep in peptideSeqList)
{
if (sequence.Contains(pep) && !finalProteinList.Contains(protein))
{
finalProteinList.Add(protein);
}
}
}
}
//test
//results: got a protein list which corresponding all peptides
//the "finalProteinList" is ready for filters.
//Console.WriteLine(proteinList.size());
//Console.WriteLine(finalProteinList.Count);
//filter by minDistinctPeptides
//filter by filterByDistinctPeptides
//filterByMinimumCoveringSet
//done it!
}
