public void WriteProteins(string outputFilepath, bool addDecoys)
{
var pd = new ProteomeData();
var pl = new ProteinListSimple();
var queryRows = session.CreateQuery("SELECT DISTINCT pro.Accession, pro.IsDecoy, pro.Description, pro.Sequence " +
DataFilter.GetFilteredQueryString(DataFilter.FromProtein))
.List <object[]>();
foreach (var queryRow in queryRows)
{
if ((bool)queryRow[1] == false) // skip decoys from the query
{
pl.proteins.Add(new proteome.Protein((string)queryRow[0],
pl.proteins.Count,
(string)queryRow[2],
(string)queryRow[3]));
}
}
if (addDecoys)
{
foreach (var queryRow in queryRows)
{
if ((bool)queryRow[1] == false) // skip decoys from the query
{
pl.proteins.Add(new proteome.Protein("rev_" + (string)queryRow[0],
pl.proteins.Count,
String.Empty, // decoys have no description
new string(((string)queryRow[3]).Reverse().ToArray())));
}
}
}
pd.proteinList = pl;
ProteomeDataFile.write(pd, outputFilepath);
}
//read a fasta database
//remove the reverse sequences
//write forward sequences into a proteinList
public static List<string> readDatabase(string database)
{
List<string> proteinList = new List<string>();
ProteomeDataFile foo = new ProteomeDataFile(database);
ProteinList p1 = foo.proteinList;
for (int i = 0; i < p1.size(); i++)
{
Protein pro = p1.protein(i, true);
if (!pro.id.Contains("rev"))
{
string sequence = p1.protein(i, true).sequence;
proteinList.Add(sequence);
}
}
return proteinList;
}
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!
}
