private static void createTestPeptideInstances (NHibernate.ISession session, BulkInserter bulkInserter, Peptide pep)
{
// store instances even though the association is inverse:
// the PeptideModification.Offset property needs access to the protein sequence
pep.Instances = new List<PeptideInstance>();
foreach (Protein pro in session.Query<Protein>())
{
int start = pro.Sequence.IndexOf(pep.Sequence, 0);
while (start >= 0)
{
int end = start + pep.Sequence.Length;
bool nTerminusIsSpecific = start == 0 || pro.Sequence[start - 1] == 'K' || pro.Sequence[start - 1] == 'R';
bool cTerminusIsSpecific = end == pro.Sequence.Length || pro.Sequence[end - 1] == 'K' || pro.Sequence[end - 1] == 'R';
var instance = new TestPI()
{
Peptide = pep,
Protein = pro,
Offset = start,
Length = pep.Sequence.Length,
MissedCleavages = pep.Sequence.ToCharArray(0, pep.Sequence.Length - 1).Count(o => o == 'K' || o == 'R'),
NTerminusIsSpecific = nTerminusIsSpecific,
CTerminusIsSpecific = cTerminusIsSpecific,
};
var instanceAccessor = new PrivateObject(instance);
instanceAccessor.SetProperty("SpecificTermini", (nTerminusIsSpecific ? 1 : 0) + (cTerminusIsSpecific ? 1 : 0));
bulkInserter.Add(instance);
pep.Instances.Add(instance);
start = pro.Sequence.IndexOf(pep.Sequence, start + 1);
}
}
if (pep.Instances.Count == 0)
throw new ArgumentException("peptide " + pep.Sequence + " does not occur in any proteins");
}
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!
}