public void SmallTest()
{
IMatrixData mdata = PerseusFactory.CreateMatrixData(new double[, ]
{
{ 0, 4 },
{ 1, 5 },
{ 2, 6 },
{ 3, 7 }
});
mdata.AddStringColumn("id", "", new [] { "a", "b", "b", "b" });
mdata.AddStringColumn("str", "", new [] { "a;b", "b;c", "c;d", "d;e" });
mdata.AddCategoryColumn("cat", "", new[] { new[] { "a", "b" }, new[] { "b", "c" }, new[] { "c", "d" }, new[] { "d", "e" } });
mdata.AddNumericColumn("num", "", new [] { 0, 1, 2, 3, 4.0 });
mdata.AddMultiNumericColumn("mnum", "", new [] { new [] { 0, 4d }, new [] { 1, 5d }, new [] { 2, 6d }, new [] { 3, 7d } });
mdata.UniqueRows(mdata.StringColumns[0], ArrayUtils.Median, UniqueRows.Union, UniqueRows.CatUnion, UniqueRows.MultiNumUnion);
Assert.AreEqual(2, mdata.RowCount);
CollectionAssert.AreEqual(new [] { 0, 2 }, mdata.Values.GetColumn(0));
CollectionAssert.AreEqual(new [] { 4, 6 }, mdata.Values.GetColumn(1));
CollectionAssert.AreEqual(new [] { "a;b", "b;c;d;e" }, mdata.GetStringColumn("str"));
CollectionAssert.AreEqual(new [] { new [] { "a", "b" }, new [] { "b", "c", "d", "e" } }, mdata.GetCategoryColumnAt(0));
CollectionAssert.AreEqual(new [] { 0, 2 }, mdata.NumericColumns[0]);
CollectionAssert.AreEqual(new [] { new [] { 0d, 4 }, new [] { 1d, 5, 2, 6, 3, 7 } }, mdata.MultiNumericColumns[0]);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
PhosphoSitePlusParser.ParseKinaseSubstrate(out string[] seqWins, out string[] subAccs, out string[] kinases, out string[] kinAccs, out string[] species);
if (seqWins == null)
{
processInfo.ErrString = "File does not exist.";
return;
}
string[] up = mdata.StringColumns[param.GetParam <int>("Uniprot column").Value];
string[][] uprot = new string[up.Length][];
for (int i = 0; i < up.Length; i++)
{
uprot[i] = up[i].Length > 0 ? up[i].Split(';') : new string[0];
}
string[] win = mdata.StringColumns[param.GetParam <int>("Sequence window").Value];
Dictionary <string, List <Tuple <string, string, string> > > substrateProperties =
new Dictionary <string, List <Tuple <string, string, string> > >();
for (int i = 0; i < seqWins.Length; i++)
{
string subAcc = subAccs[i];
if (!substrateProperties.ContainsKey(subAcc))
{
substrateProperties.Add(subAcc, new List <Tuple <string, string, string> >());
}
substrateProperties[subAcc].Add(new Tuple <string, string, string>(seqWins[i], kinases[i], kinAccs[i]));
}
string[] kinaseNameColumn = new string[uprot.Length];
string[] kinaseUniprotColumn = new string[uprot.Length];
for (int i = 0; i < kinaseNameColumn.Length; i++)
{
string[] win1 = AddKnownSites.TransformIl(win[i]).Split(';');
HashSet <string> kinaseNamesHits = new HashSet <string>();
HashSet <string> kinaseUniprotHits = new HashSet <string>();
foreach (string ux in uprot[i])
{
if (substrateProperties.ContainsKey(ux))
{
List <Tuple <string, string, string> > properties = substrateProperties[ux];
foreach (Tuple <string, string, string> property in properties)
{
string w = property.Item1;
if (AddKnownSites.Contains(win1, AddKnownSites.TransformIl(w.ToUpper().Substring(1, w.Length - 2))))
{
kinaseNamesHits.Add(property.Item2);
kinaseUniprotHits.Add(property.Item3);
}
}
}
}
kinaseNameColumn[i] = kinaseNamesHits.Count > 0 ? StringUtils.Concat(";", ArrayUtils.ToArray(kinaseNamesHits)) : "";
kinaseUniprotColumn[i] = kinaseUniprotHits.Count > 0
? StringUtils.Concat(";", ArrayUtils.ToArray(kinaseUniprotHits))
: "";
}
mdata.AddStringColumn("PhosphoSitePlus kinase", "", kinaseNameColumn);
mdata.AddStringColumn("PhosphoSitePlus kinase uniprot", "", kinaseUniprotColumn);
}
public void TestInitialize()
{
var peptidesValues = new[, ] {
{ 9.0f }
};
peptides = PerseusFactory.CreateMatrixData(peptidesValues, new List <string> {
"pep_MS/MS Count"
});
peptides.AddNumericColumn("pep_Intensity", "", new [] { 0.0 });
peptides.AddStringColumn("pep_id", "", new [] { "35" });
peptides.AddStringColumn("pep_Protein group IDs", "", new [] { "13;21" });
peptides.Quality.Init(1, 1);
peptides.Quality.Set(0, 0, 1);
var multiNum = new ExpandMultiNumeric();
var errorString = string.Empty;
var parameters2 = multiNum.GetParameters(peptides, ref errorString);
parameters2.GetParam <int[]>("Text columns").Value = new[] { 1 };
IMatrixData[] suppl = null;
IDocumentData[] docs = null;
multiNum.ProcessData(peptides, parameters2, ref suppl, ref docs, CreateProcessInfo());
var proteinMainValues = new[, ]
{
{ 166250000.0f },
{ 8346000.0f }
};
proteinMain = PerseusFactory.CreateMatrixData(proteinMainValues, new List <string> {
"prot_LFQ intensity"
});
proteinMain.Name = "protein main";
proteinMain.AddStringColumn("prot_id", "", new [] { "13", "21" });
proteinMain.AddStringColumn("prot_gene name", "", new [] { "geneA", "geneB" });
var expandValues = new[, ]
{
{ 9.0f },
{ 9.0f }
};
expand = PerseusFactory.CreateMatrixData(expandValues, new List <string> {
"pep_MS/MS Count"
});
expand.Name = "expand";
expand.AddNumericColumn("pep_Intensity", "", new [] { 0.0, 0.0 });
expand.AddStringColumn("pep_id", "", new [] { "35", "35" });
expand.AddStringColumn("pep_Protein group IDs", "", new [] { "13", "21" });
matching = new MatchingRowsByName();
var err = string.Empty;
parameters = matching.GetParameters(new[] { expand, proteinMain }, ref err);
}
public void WriteMatrixTest()
{
// main data
IMatrixData mdata = PerseusFactory.CreateMatrixData(new double[, ] {
{ 1, 2, 3 }, { 3, 4, 5 }
},
new List <string> {
"col1", "col2", "col3"
});
// annotation rows
mdata.AddCategoryRow("catrow", "this is catrow", new[] { new[] { "cat1" }, new[] { "cat1", "cat2" }, new[] { "cat2" } });
mdata.AddNumericRow("numrow", "this is numrow", new[] { -1.0, 1, 2 });
// annotation columns
mdata.AddStringColumn("strcol1", "this is stringcol1", new[] { "1", "2" });
mdata.AddStringColumn("strcol2", "", new[] { "", "hallo" });
mdata.AddNumericColumn("numcol", "", new[] { 1.0, 2.0 });
mdata.AddMultiNumericColumn("multnumcol", "this is multnumcol", new[] { new[] { -2.0, 2.0 }, new double[] {} });
mdata.AddCategoryColumn("catcol", "", new[] { new[] { "cat1", "cat1.1" }, new[] { "cat2", "cat1" } });
string mdataStr;
using (MemoryStream memstream = new MemoryStream())
using (StreamWriter writer = new StreamWriter(memstream)) {
PerseusUtils.WriteMatrix(mdata, writer);
writer.Flush();
mdataStr = Encoding.UTF8.GetString(memstream.ToArray());
}
IMatrixData mdata2 = PerseusFactory.CreateMatrixData();
PerseusUtils.ReadMatrix(mdata2, new ProcessInfo(new Settings(), status => { }, progress => { }, 1), () => {
StreamReader tmpStream = new StreamReader(new MemoryStream(Encoding.UTF8.GetBytes(mdataStr)));
return(tmpStream);
}, "matrix1", '\t');
Assert.AreEqual(2, mdata2.RowCount);
Assert.AreEqual(3, mdata2.ColumnCount);
Assert.AreEqual(2, mdata2.StringColumnCount);
Assert.AreEqual(1, mdata2.NumericColumnCount);
Assert.AreEqual(1, mdata2.CategoryColumnCount);
Assert.AreEqual(1, mdata2.MultiNumericColumnCount);
Assert.AreEqual("hallo", mdata2.StringColumns[mdata2.StringColumnNames.FindIndex(col => col.Equals("strcol2"))][1]);
Assert.AreEqual(1, mdata2.CategoryRowCount);
Assert.AreEqual(1, mdata2.NumericRowCount);
}
public void ProcessData(IMatrixData mdata, Parameters para, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
string[] baseIds = GetBaseIds(para, mdata);
string[] name;
int[] catColInds;
int[] textColInds;
int[] numColInds;
string[][][] catCols;
string[][] textCols;
double[][] numCols;
bool success = ProcessDataAddAnnotation(mdata.RowCount, para, baseIds, processInfo, out name, out catColInds,
out textColInds, out numColInds, out catCols, out textCols, out numCols);
if (!success)
{
return;
}
for (int i = 0; i < catCols.Length; i++)
{
mdata.AddCategoryColumn(name[catColInds[i]], "", catCols[i]);
}
for (int i = 0; i < textCols.Length; i++)
{
mdata.AddStringColumn(name[textColInds[i]], "", textCols[i]);
}
for (int i = 0; i < numCols.Length; i++)
{
mdata.AddNumericColumn(name[numColInds[i]], "", numCols[i]);
}
}
public void Setup()
{
_mdata = PerseusFactory.CreateMatrixData(new[, ] {
{ 0.0, 1.0, 0.0 }, { 0.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }
});
_mdata.AddStringColumn("test", "", new [] { "a", "b", "a" });
}
public void ProcessData(IMatrixData mdata, Parameters para, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
GetAvailableTextAnnots(out string[] baseNames, out int[][] inds, out string[] files);
ParameterWithSubParams <int> spd = para.GetParamWithSubParams <int>("Source");
int ind = spd.Value;
Parameters param = spd.GetSubParameters();
int baseCol = param.GetParam <int>("Identifiers").Value;
int selection = param.GetParam <int>("Identifier type").Value;
HashSet <string> allIds = GetAllIds(mdata, baseCol);
string file = files[ind];
Dictionary <string, string[]> mapping = ReadMapping(allIds, file, inds[ind][selection]);
string[] x = mdata.StringColumns[baseCol];
string[] newCol = new string[x.Length];
for (int i = 0; i < x.Length; i++)
{
string w = x[i];
string[] q = w.Length > 0 ? w.Split(';') : new string[0];
List <string> m = new List <string>();
foreach (string s in q)
{
string r = s.ToLower();
if (mapping.ContainsKey(r))
{
m.AddRange(mapping[r]);
}
}
string[] vals = ArrayUtils.UniqueValues(m);
newCol[i] = StringUtils.Concat(";", vals);
}
mdata.AddStringColumn(baseNames[ind], baseNames[ind], newCol);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int stringColumnIndx = param.GetParam <int>("Sequence window").Value;
string[] win = mdata.StringColumns[stringColumnIndx];
int start = param.GetParam <int>("Start").Value - 1;
int length = param.GetParam <int>("Length").Value;
if (start < 0)
{
processInfo.ErrString = "Start position cannot be smaller than 1.";
return;
}
if (start + length > win[0].Length)
{
processInfo.ErrString = "Start + length cannot exceed the total length of the sequence.";
return;
}
string[] shortenedMotifs = new string[win.Length];
for (int i = 0; i < mdata.RowCount; ++i)
{
shortenedMotifs[i] = win[i].Substring(start, length);
}
mdata.AddStringColumn("Short sequence window", "", shortenedMotifs);
}
public void ProcessData(IMatrixData data, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] exColInds = param.GetParam <int[]>("Main columns").Value;
int[] numColInds = param.GetParam <int[]>("Numerical columns").Value;
int[] multiNumColInds = param.GetParam <int[]>("Multi-numerical columns").Value;
int[] catColInds = param.GetParam <int[]>("Categorical columns").Value;
int[] textColInds = param.GetParam <int[]>("Text columns").Value;
if (exColInds.Length > 0)
{
int ncol = data.ColumnCount;
data.ExtractColumns(ArrayUtils.Concat(ArrayUtils.ConsecutiveInts(data.ColumnCount), exColInds));
HashSet <string> taken = new HashSet <string>(data.ColumnNames);
for (int i = 0; i < exColInds.Length; i++)
{
string s = StringUtils.GetNextAvailableName(data.ColumnNames[ncol + i], taken);
data.ColumnNames[ncol + i] = s;
taken.Add(s);
}
}
foreach (int ind in numColInds)
{
HashSet <string> taken = new HashSet <string>(data.NumericColumnNames);
string s = StringUtils.GetNextAvailableName(data.NumericColumnNames[ind], taken);
data.AddNumericColumn(s, data.NumericColumnDescriptions[ind], (double[])data.NumericColumns[ind].Clone());
taken.Add(s);
}
foreach (int ind in multiNumColInds)
{
HashSet <string> taken = new HashSet <string>(data.MultiNumericColumnNames);
string s = StringUtils.GetNextAvailableName(data.MultiNumericColumnNames[ind], taken);
data.AddMultiNumericColumn(s, data.MultiNumericColumnDescriptions[ind],
(double[][])data.MultiNumericColumns[ind].Clone());
taken.Add(s);
}
foreach (int ind in catColInds)
{
HashSet <string> taken = new HashSet <string>(data.CategoryColumnNames);
string s = StringUtils.GetNextAvailableName(data.CategoryColumnNames[ind], taken);
data.AddCategoryColumn(s, data.CategoryColumnDescriptions[ind], data.GetCategoryColumnAt(ind));
taken.Add(s);
}
foreach (int ind in textColInds)
{
HashSet <string> taken = new HashSet <string>(data.StringColumnNames);
string s = StringUtils.GetNextAvailableName(data.StringColumnNames[ind], taken);
data.AddStringColumn(s, data.ColumnDescriptions[ind], (string[])data.StringColumns[ind].Clone());
taken.Add(s);
}
}
public void ProcessData(IMatrixData mdata, Parameters para, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
var annotationProvider = _annotationProvider;
ParameterWithSubParams <int> sourceParam = para.GetParamWithSubParams <int>("Source");
int sourceIndex = sourceParam.Value;
Parameters param = sourceParam.GetSubParameters();
int baseCol = param.GetParam <int>("Identifiers").Value;
int selection = param.GetParam <int>("Identifier type").Value;
var(_, id, _) = annotationProvider.TextSources()[sourceIndex];
var newColumn = annotationProvider.MapToBaseIdentifiers(mdata.StringColumns[baseCol], sourceIndex, selection);
mdata.AddStringColumn(id, id, newColumn);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] inds = param.GetParam <int[]>("Columns").Value;
bool keepColumns = param.GetParam <bool>("Keep original columns").Value;
foreach (var col in inds)
{
var values = mdata.StringColumns[col].Select(s => s.ToUpper()).ToArray();
if (keepColumns)
{
mdata.AddStringColumn(mdata.StringColumnNames[col], mdata.StringColumnDescriptions[col], values);
}
else
{
mdata.StringColumns[col] = values;
}
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int stringColumnIndx = param.GetParam<int>("Sequence window").Value;
string[] win = mdata.StringColumns[stringColumnIndx];
int start = param.GetParam<int>("Start").Value - 1;
int length = param.GetParam<int>("Length").Value;
if (start < 0){
processInfo.ErrString = "Start position cannot be smaller than 1.";
return;
}
if (start + length > win[0].Length){
processInfo.ErrString = "Start + length cannot exceed the total length of the sequence.";
return;
}
string[] shortenedMotifs = new string[win.Length];
for (int i = 0; i < mdata.RowCount; ++i){
shortenedMotifs[i] = win[i].Substring(start, length);
}
mdata.AddStringColumn("Short sequence window", "", shortenedMotifs);
}
public void TestSmallExample()
{
double[,] values = new[, ]
{
{ 0.0, 1.0, 0, 5 },
{ 2.0, 3.0, 0, 5 }
};
IMatrixData mdata = PerseusFactory.CreateMatrixData(values, new List <string> {
"Col___1", "Col___2", "Col___3", "No expand"
});
mdata.ColumnDescriptions = new List <string> {
"Description Col", "Col", "Col", "Description No expand"
};
double[][] multiNum = new[]
{
new[] { 0.0, 1.0 },
new[] { 2.0 }
};
mdata.AddMultiNumericColumn("MultiNum", "", multiNum);
string[] stringCol = new[] { "row1", "row2" };
mdata.AddStringColumn("String", "", stringCol);
ExpandSiteTable expand = new ExpandSiteTable();
IMatrixData[] supplData = null;
IDocumentData[] docs = null;
expand.ProcessData(mdata, new Parameters(), ref supplData, ref docs, CreateProcessInfo());
Assert.AreEqual(2, mdata.ColumnCount);
CollectionAssert.AreEqual(new [] { "No expand", "Col" }, mdata.ColumnNames.ToArray());
Assert.AreEqual(2, mdata.ColumnDescriptions.Count);
CollectionAssert.AreEqual(new [] { "Description No expand", "Description Col" }, mdata.ColumnDescriptions.ToArray());
Assert.AreEqual(6, mdata.RowCount);
Assert.AreEqual(2, mdata.StringColumnCount);
CollectionAssert.AreEqual(new [] { "String", "Unique identifier" }, mdata.StringColumnNames);
CollectionAssert.AreEqual(stringCol.Concat(stringCol).Concat(stringCol).ToArray(), mdata.StringColumns[0]);
Assert.AreEqual(1, mdata.MultiNumericColumnCount);
CollectionAssert.AreEqual(multiNum.Concat(multiNum).Concat(multiNum).ToArray(), mdata.MultiNumericColumns[0]);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
string mod = param.GetParam <int>("Modification").StringValue;
PhosphoSitePlusParser.ParseKnownMod(mod, out string[] seqWins, out string[] accs, out string[] pubmedLtp, out string[] pubmedMs2, out string[] cstMs2, out string[] species);
if (seqWins == null)
{
processInfo.ErrString = "File does not exist.";
return;
}
string[] up = mdata.StringColumns[param.GetParam <int>("Uniprot column").Value];
string[][] uprot = new string[up.Length][];
for (int i = 0; i < up.Length; i++)
{
uprot[i] = up[i].Length > 0 ? up[i].Split(';') : new string[0];
}
string[] win = mdata.StringColumns[param.GetParam <int>("Sequence window").Value];
Dictionary <string, List <int> > map = new Dictionary <string, List <int> >();
for (int i = 0; i < seqWins.Length; i++)
{
string acc = accs[i];
if (!map.ContainsKey(acc))
{
map.Add(acc, new List <int>());
}
map[acc].Add(i);
}
string[] newCol = new string[uprot.Length];
string[][] newCatCol = new string[uprot.Length][];
string[][] originCol = new string[uprot.Length][];
for (int i = 0; i < newCol.Length; i++)
{
string[] win1 = TransformIl(win[i]).Split(';');
HashSet <string> wins = new HashSet <string>();
HashSet <string> origins = new HashSet <string>();
foreach (string ux in uprot[i])
{
if (map.ContainsKey(ux))
{
List <int> n = map[ux];
foreach (int ind in n)
{
string s = seqWins[ind];
if (Contains(win1, TransformIl(s.ToUpper().Substring(1, s.Length - 2))))
{
wins.Add(s);
if (pubmedLtp[ind].Length > 0)
{
origins.Add("LTP");
}
if (pubmedMs2[ind].Length > 0)
{
origins.Add("HTP");
}
if (cstMs2[ind].Length > 0)
{
origins.Add("CST");
}
}
}
}
}
if (wins.Count > 0)
{
newCol[i] = StringUtils.Concat(";", ArrayUtils.ToArray(wins));
newCatCol[i] = new[] { "+" };
string[] x = ArrayUtils.ToArray(origins);
Array.Sort(x);
originCol[i] = x;
}
else
{
newCol[i] = "";
newCatCol[i] = new string[0];
originCol[i] = new string[0];
}
}
mdata.AddStringColumn("PhosphoSitePlus window", "", newCol);
mdata.AddCategoryColumn("Known site", "", newCatCol);
mdata.AddCategoryColumn("Origin", "", originCol);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int proteinIdColumnInd = param.GetParam<int>("Protein IDs").Value;
string[][] proteinIds = new string[mdata.RowCount][];
string[][] leadingIds = new string[mdata.RowCount][];
List<string> allIds = new List<string>();
for (int row = 0; row < mdata.RowCount; row++){
proteinIds[row] = mdata.StringColumns[proteinIdColumnInd][row].Split(';');
leadingIds[row] = new[]{proteinIds[row][0]};
allIds.AddRange(proteinIds[row]);
}
string fastaFilePath = param.GetParam<string>("Fasta file").Value;
Fasta fasta = new Fasta();
fasta.ParseFile(fastaFilePath, processInfo);
// Text annotations
processInfo.Status("Adding fasta header annotations.");
int[] selection =
param.GetParamWithSubParams<int>("Fasta header annotations").GetSubParameters().GetParam<int[]>("Annotations").Value;
string[][] idsToBeAnnotated = (param.GetParamWithSubParams<int>("Fasta header annotations").Value == 0)
? proteinIds
: leadingIds;
ProteinSequence[][] fastaEntries = new ProteinSequence[mdata.RowCount][];
for (int row = 0; row < mdata.RowCount; row++){
List<ProteinSequence> rowEntries = new List<ProteinSequence>();
foreach (string id in idsToBeAnnotated[row]){
ProteinSequence entry = fasta.GetEntry(id);
if (entry == null){
continue;
}
rowEntries.Add(entry);
}
fastaEntries[row] = rowEntries.ToArray();
}
if (ArrayUtils.Contains(selection, 0)){ // Entry name
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<string> rowAnnotations = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
string entryName = entry.EntryName;
if (entryName != null && !ArrayUtils.Contains(rowAnnotations, entryName)){
rowAnnotations.Add(entryName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Entry name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 1)){ // Gene name
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<string> rowAnnotations = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
string geneName = entry.GeneName;
if (geneName != null && !ArrayUtils.Contains(rowAnnotations, geneName)){
rowAnnotations.Add(geneName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Gene name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 2)){
// Verbose protein name, i.e. all protein names annotated in all fasta headers, including the
//'Isoform x of...' prefixes and '(Fragment)' suffixes
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<string> rowAnnotations = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
string proteinName = entry.ProteinName;
if (proteinName != null && !ArrayUtils.Contains(rowAnnotations, proteinName)){
rowAnnotations.Add(proteinName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Protein name (verbose)", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 3)){ // Consensus protein name
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<string> rowAnnotations = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
string proteinName = entry.ConsensusProteinName;
if (proteinName != null && !ArrayUtils.Contains(rowAnnotations, proteinName)){
rowAnnotations.Add(proteinName);
}
}
annotationColumn[row] = String.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Protein name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 4)){ // Species
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<string> rowAnnotations = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
string speciesName = entry.Species;
if (speciesName != null && !ArrayUtils.Contains(rowAnnotations, speciesName)){
rowAnnotations.Add(speciesName);
}
}
annotationColumn[row] = String.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Species", "", annotationColumn);
}
// Numeric annotations
processInfo.Status("Adding numeric annotations.");
selection =
param.GetParamWithSubParams<int>("Numeric annotations").GetSubParameters().GetParam<int[]>("Annotations").Value;
bool annotateLeadingId = (param.GetParamWithSubParams<int>("Numeric annotations").Value == 1);
if (ArrayUtils.Contains(selection, 0)){ // Sequence length
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<double> rowAnnotations = new List<double>();
foreach (ProteinSequence entry in fastaEntries[row]){
double sequenceLength = entry.GetSequence().Length;
rowAnnotations.Add(sequenceLength);
if (annotateLeadingId && rowAnnotations.Count > 0){
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Sequence length", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 1)){ // Monoisotopic molecular mass
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<double> rowAnnotations = new List<double>();
foreach (ProteinSequence entry in fastaEntries[row]){
double monoisotopicMass = entry.GetMonoisotopicMolecularMass();
rowAnnotations.Add(monoisotopicMass);
if (annotateLeadingId && rowAnnotations.Count > 0){
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Monoisotopic molecular mass", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 2)){ // Average molecular mass
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<double> rowAnnotations = new List<double>();
foreach (ProteinSequence entry in fastaEntries[row]){
double averageMass = entry.GetAverageMolecularMass();
rowAnnotations.Add(averageMass);
if (annotateLeadingId && rowAnnotations.Count > 0){
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Average molecular mass", "", annotationColumn);
}
// Theoretical peptides
processInfo.Status("Calculating theoretical peptides.");
annotateLeadingId = (param.GetParamWithSubParams<int>("Calculate theoretical peptides").Value == 1);
Protease[] proteases = ArrayUtils.SubArray(Constants.defaultProteases,
param.GetParamWithSubParams<int>("Calculate theoretical peptides").GetSubParameters().GetParam<int[]>("Proteases")
.Value);
double minLength =
param.GetParamWithSubParams<int>("Calculate theoretical peptides").GetSubParameters().GetParam<double>(
"Min. peptide length").Value;
double maxLength =
param.GetParamWithSubParams<int>("Calculate theoretical peptides").GetSubParameters().GetParam<double>(
"Max. peptide length").Value;
bool displayPeptideSequences = annotateLeadingId &&
param.GetParamWithSubParams<int>("Calculate theoretical peptides").GetSubParameters().GetParam<bool>(
"Show sequences").Value;
foreach (Protease protease in proteases){
double[] annotationColumn = new double[mdata.RowCount];
string[] peptideColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<double> rowAnnotations = new List<double>();
List<string> rowPeptides = new List<string>();
foreach (ProteinSequence entry in fastaEntries[row]){
double nTheoreticalPeptides = entry.GetNumberOfTheoreticalPeptides(protease, (int) minLength, (int) maxLength);
rowAnnotations.Add(nTheoreticalPeptides);
if (displayPeptideSequences){
rowPeptides.AddRange(entry.GetTheoreticalPeptideSequences(protease, (int) minLength, (int) maxLength));
}
if (annotateLeadingId && rowAnnotations.Count > 0){
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
peptideColumn[row] = String.Join(";", rowPeptides);
}
mdata.AddNumericColumn(
"Number of theoretical peptides (" + protease.name + ", " + minLength + "-" + maxLength + ")", "", annotationColumn);
if (displayPeptideSequences){
mdata.AddStringColumn(
"Theoretical peptide sequences (" + protease.name + ", " + minLength + "-" + maxLength + ")", "", peptideColumn);
}
}
// Sequence features
processInfo.Status("Counting sequence features.");
annotateLeadingId = (param.GetParamWithSubParams<int>("Count sequence features").Value == 1);
bool normalizeBySequenceLength =
param.GetParamWithSubParams<int>("Count sequence features").GetSubParameters().GetParam<bool>(
"Normalize by sequence length").Value;
if (param.GetParamWithSubParams<int>("Count sequence features").GetSubParameters().GetParam<string>("Regex").Value !=
""){
Regex regex;
try{
regex =
new Regex(
param.GetParamWithSubParams<int>("Count sequence features").GetSubParameters().GetParam<string>("Regex").Value);
} catch (ArgumentException){
processInfo.ErrString = "The regular expression you provided has invalid syntax.";
return;
}
double[] sequenceFeatureColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++){
List<double> featureCount = new List<double>();
foreach (ProteinSequence entry in fastaEntries[row]){
double nFeatures = regex.Matches(entry.GetSequence()).Count;
featureCount.Add(normalizeBySequenceLength ? nFeatures/entry.GetLength() : nFeatures);
if (annotateLeadingId){
break;
}
}
sequenceFeatureColumn[row] = ArrayUtils.Median(featureCount.ToArray());
}
mdata.AddNumericColumn(
(normalizeBySequenceLength ? "Normalized feature count (" : "Feature count (") + regex + ")", "",
sequenceFeatureColumn);
}
processInfo.Status("Done.");
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
string[] seqWins;
string[] subAccs;
string[] kinases;
string[] kinAccs;
string[] species;
PhosphoSitePlusParser.ParseKinaseSubstrate(out seqWins, out subAccs, out kinases, out kinAccs, out species);
if (seqWins == null){
processInfo.ErrString = "File does not exist.";
return;
}
string[] up = mdata.StringColumns[param.GetParam<int>("Uniprot column").Value];
string[][] uprot = new string[up.Length][];
for (int i = 0; i < up.Length; i++){
uprot[i] = up[i].Length > 0 ? up[i].Split(';') : new string[0];
}
string[] win = mdata.StringColumns[param.GetParam<int>("Sequence window").Value];
Dictionary<string, List<Tuple<string, string, string>>> substrateProperties =
new Dictionary<string, List<Tuple<string, string, string>>>();
for (int i = 0; i < seqWins.Length; i++){
string subAcc = subAccs[i];
if (!substrateProperties.ContainsKey(subAcc)){
substrateProperties.Add(subAcc, new List<Tuple<string, string, string>>());
}
substrateProperties[subAcc].Add(new Tuple<string, string, string>(seqWins[i], kinases[i], kinAccs[i]));
}
string[] kinaseNameColumn = new string[uprot.Length];
string[] kinaseUniprotColumn = new string[uprot.Length];
for (int i = 0; i < kinaseNameColumn.Length; i++){
string[] win1 = AddKnownSites.TransformIl(win[i]).Split(';');
HashSet<string> kinaseNamesHits = new HashSet<string>();
HashSet<string> kinaseUniprotHits = new HashSet<string>();
foreach (string ux in uprot[i]){
if (substrateProperties.ContainsKey(ux)){
List<Tuple<string, string, string>> properties = substrateProperties[ux];
foreach (Tuple<string, string, string> property in properties){
string w = property.Item1;
if (AddKnownSites.Contains(win1, AddKnownSites.TransformIl(w.ToUpper().Substring(1, w.Length - 2)))){
kinaseNamesHits.Add(property.Item2);
kinaseUniprotHits.Add(property.Item3);
}
}
}
}
kinaseNameColumn[i] = kinaseNamesHits.Count > 0 ? StringUtils.Concat(";", ArrayUtils.ToArray(kinaseNamesHits)) : "";
kinaseUniprotColumn[i] = kinaseUniprotHits.Count > 0
? StringUtils.Concat(";", ArrayUtils.ToArray(kinaseUniprotHits))
: "";
}
mdata.AddStringColumn("PhosphoSitePlus kinase", "", kinaseNameColumn);
mdata.AddStringColumn("PhosphoSitePlus kinase uniprot", "", kinaseUniprotColumn);
}
public IMatrixData ProcessData(IMatrixData[] inputData, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
IMatrixData mdata1 = inputData[0];
IMatrixData mdata2 = inputData[1];
string[] header1 = new string[mdata1.RowCount];
for (int i = 0; i < mdata1.RowCount; i++)
{
header1[i] = mdata1.Name;
}
string[] header2 = new string[mdata2.RowCount];
for (int i = 0; i < mdata2.RowCount; i++)
{
header2[i] = mdata2.Name;
}
int nrows1 = mdata1.RowCount;
int nrows2 = mdata2.RowCount;
int nrows = nrows1 + nrows2;
string[] expColNames = SpecialSort(mdata1.ColumnNames, mdata2.ColumnNames, out Dictionary <string, int> dic1, out Dictionary <string, int> dic2);
double[,] ex = new double[nrows, expColNames.Length];
for (int i = 0; i < ex.GetLength(0); i++)
{
for (int j = 0; j < ex.GetLength(1); j++)
{
ex[i, j] = double.NaN;
}
}
for (int i = 0; i < expColNames.Length; i++)
{
if (dic1.ContainsKey(expColNames[i]))
{
int ind = dic1[expColNames[i]];
for (int j = 0; j < nrows1; j++)
{
ex[j, i] = mdata1.Values.Get(j, ind);
}
}
if (dic2.ContainsKey(expColNames[i]))
{
int ind = dic2[expColNames[i]];
for (int j = 0; j < nrows2; j++)
{
ex[nrows1 + j, i] = mdata2.Values.Get(j, ind);
}
}
}
string[] numColNames = SpecialSort(mdata1.NumericColumnNames, mdata2.NumericColumnNames, out dic1, out dic2);
List <double[]> numCols = new List <double[]>();
for (int i = 0; i < numColNames.Length; i++)
{
numCols.Add(new double[nrows]);
for (int j = 0; j < nrows; j++)
{
numCols[numCols.Count - 1][j] = double.NaN;
}
}
for (int i = 0; i < numColNames.Length; i++)
{
if (dic1.ContainsKey(numColNames[i]))
{
int ind = dic1[numColNames[i]];
for (int j = 0; j < nrows1; j++)
{
numCols[i][j] = mdata1.NumericColumns[ind][j];
}
}
if (dic2.ContainsKey(numColNames[i]))
{
int ind = dic2[numColNames[i]];
for (int j = 0; j < nrows2; j++)
{
numCols[i][nrows1 + j] = mdata2.NumericColumns[ind][j];
}
}
}
string[] stringColNames = SpecialSort(mdata1.StringColumnNames, mdata2.StringColumnNames, out dic1, out dic2);
List <string[]> stringCols = new List <string[]>();
for (int i = 0; i < stringColNames.Length; i++)
{
stringCols.Add(new string[nrows]);
for (int j = 0; j < nrows; j++)
{
stringCols[stringCols.Count - 1][j] = "";
}
}
for (int i = 0; i < stringColNames.Length; i++)
{
if (dic1.ContainsKey(stringColNames[i]))
{
int ind = dic1[stringColNames[i]];
for (int j = 0; j < nrows1; j++)
{
stringCols[i][j] = mdata1.StringColumns[ind][j];
}
}
if (dic2.ContainsKey(stringColNames[i]))
{
int ind = dic2[stringColNames[i]];
for (int j = 0; j < nrows2; j++)
{
stringCols[i][nrows1 + j] = mdata2.StringColumns[ind][j];
}
}
}
string[] catColNames = SpecialSort(mdata1.CategoryColumnNames, mdata2.CategoryColumnNames, out dic1, out dic2);
List <string[][]> catCols = new List <string[][]>();
for (int i = 0; i < catColNames.Length; i++)
{
catCols.Add(new string[nrows][]);
for (int j = 0; j < nrows; j++)
{
catCols[catCols.Count - 1][j] = new string[0];
}
}
for (int i = 0; i < catColNames.Length; i++)
{
if (dic1.ContainsKey(catColNames[i]))
{
int ind = dic1[catColNames[i]];
for (int j = 0; j < nrows1; j++)
{
catCols[i][j] = mdata1.GetCategoryColumnEntryAt(ind, j);
}
}
if (dic2.ContainsKey(catColNames[i]))
{
int ind = dic2[catColNames[i]];
for (int j = 0; j < nrows2; j++)
{
catCols[i][nrows1 + j] = mdata2.GetCategoryColumnEntryAt(ind, j);
}
}
}
string[] multiNumColNames = SpecialSort(mdata1.MultiNumericColumnNames, mdata2.MultiNumericColumnNames, out dic1,
out dic2);
List <double[][]> multiNumCols = new List <double[][]>();
for (int i = 0; i < multiNumColNames.Length; i++)
{
multiNumCols.Add(new double[nrows][]);
for (int j = 0; j < nrows; j++)
{
multiNumCols[multiNumCols.Count - 1][j] = new double[0];
}
}
for (int i = 0; i < multiNumColNames.Length; i++)
{
if (dic1.ContainsKey(multiNumColNames[i]))
{
int ind = dic1[multiNumColNames[i]];
for (int j = 0; j < nrows1; j++)
{
multiNumCols[i][j] = mdata1.MultiNumericColumns[ind][j];
}
}
if (dic2.ContainsKey(multiNumColNames[i]))
{
int ind = dic2[multiNumColNames[i]];
for (int j = 0; j < nrows2; j++)
{
multiNumCols[i][nrows1 + j] = mdata2.MultiNumericColumns[ind][j];
}
}
}
string MatrixName = "Matrix Name";
string MatrixDescription = "Description";
string[] listnames = header1.Concat(header2).ToArray();
// string[][] resultarray = catlistnames.Select(x => x.ToArray()).ToArray();
//IMPORTANT!!!!! TODO: check if the name of the matrix if changed
IMatrixData result = PerseusFactory.CreateMatrixData(ex, expColNames.ToList());
result.NumericColumnNames = new List <string>(numColNames);
result.NumericColumnDescriptions = result.NumericColumnNames;
result.NumericColumns = numCols;
result.StringColumnNames = new List <string>(stringColNames);
result.StringColumns = stringCols;
result.CategoryColumnNames = new List <string>(catColNames);
result.CategoryColumnDescriptions = result.CategoryColumnNames;
result.CategoryColumns = catCols;
result.MultiNumericColumnNames = new List <string>(multiNumColNames);
result.MultiNumericColumnDescriptions = result.MultiNumericColumnNames;
result.MultiNumericColumns = multiNumCols;
HashSet <string> taken = new HashSet <string>(result.StringColumnNames);
result.AddStringColumn(MatrixName, MatrixName, listnames);
taken.Add(MatrixName);
return(result);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
string mod = param.GetParam<int>("Modification").StringValue;
string[] seqWins;
string[] accs;
string[] pubmedLtp;
string[] pubmedMs2;
string[] cstMs2;
string[] species;
PhosphoSitePlusParser.ParseKnownMod(mod, out seqWins, out accs, out pubmedLtp, out pubmedMs2, out cstMs2, out species);
if (seqWins == null){
processInfo.ErrString = "File does not exist.";
return;
}
string[] up = mdata.StringColumns[param.GetParam<int>("Uniprot column").Value];
string[][] uprot = new string[up.Length][];
for (int i = 0; i < up.Length; i++){
uprot[i] = up[i].Length > 0 ? up[i].Split(';') : new string[0];
}
string[] win = mdata.StringColumns[param.GetParam<int>("Sequence window").Value];
Dictionary<string, List<int>> map = new Dictionary<string, List<int>>();
for (int i = 0; i < seqWins.Length; i++){
string acc = accs[i];
if (!map.ContainsKey(acc)){
map.Add(acc, new List<int>());
}
map[acc].Add(i);
}
string[] newCol = new string[uprot.Length];
string[][] newCatCol = new string[uprot.Length][];
string[][] originCol = new string[uprot.Length][];
for (int i = 0; i < newCol.Length; i++){
string[] win1 = TransformIl(win[i]).Split(';');
HashSet<string> wins = new HashSet<string>();
HashSet<string> origins = new HashSet<string>();
foreach (string ux in uprot[i]){
if (map.ContainsKey(ux)){
List<int> n = map[ux];
foreach (int ind in n){
string s = seqWins[ind];
if (Contains(win1, TransformIl(s.ToUpper().Substring(1, s.Length - 2)))){
wins.Add(s);
if (pubmedLtp[ind].Length > 0){
origins.Add("LTP");
}
if (pubmedMs2[ind].Length > 0){
origins.Add("HTP");
}
if (cstMs2[ind].Length > 0){
origins.Add("CST");
}
}
}
}
}
if (wins.Count > 0){
newCol[i] = StringUtils.Concat(";", ArrayUtils.ToArray(wins));
newCatCol[i] = new[]{"+"};
string[] x = ArrayUtils.ToArray(origins);
Array.Sort(x);
originCol[i] = x;
} else{
newCol[i] = "";
newCatCol[i] = new string[0];
originCol[i] = new string[0];
}
}
mdata.AddStringColumn("PhosphoSitePlus window", "", newCol);
mdata.AddCategoryColumn("Known site", "", newCatCol);
mdata.AddCategoryColumn("Origin", "", originCol);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int proteinIdColumnInd = param.GetParam <int>("Protein IDs").Value;
string[][] proteinIds = new string[mdata.RowCount][];
string[][] leadingIds = new string[mdata.RowCount][];
List <string> allIds = new List <string>();
for (int row = 0; row < mdata.RowCount; row++)
{
proteinIds[row] = mdata.StringColumns[proteinIdColumnInd][row].Split(';');
leadingIds[row] = new[] { proteinIds[row][0] };
allIds.AddRange(proteinIds[row]);
}
string fastaFilePath = param.GetParam <string>("Fasta file").Value;
Fasta fasta = new Fasta();
fasta.ParseFile(fastaFilePath, processInfo);
// Text annotations
processInfo.Status("Adding fasta header annotations.");
int[] selection =
param.GetParamWithSubParams <int>("Fasta header annotations").GetSubParameters().GetParam <int[]>("Annotations").Value;
string[][] idsToBeAnnotated = param.GetParamWithSubParams <int>("Fasta header annotations").Value == 0
? proteinIds
: leadingIds;
ProteinSequence[][] fastaEntries = new ProteinSequence[mdata.RowCount][];
for (int row = 0; row < mdata.RowCount; row++)
{
List <ProteinSequence> rowEntries = new List <ProteinSequence>();
foreach (string id in idsToBeAnnotated[row])
{
ProteinSequence entry = fasta.GetEntry(id);
if (entry == null)
{
continue;
}
rowEntries.Add(entry);
}
fastaEntries[row] = rowEntries.ToArray();
}
if (ArrayUtils.Contains(selection, 0)) // Entry name
{
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <string> rowAnnotations = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
string entryName = entry.EntryName;
if (entryName != null && !ArrayUtils.Contains(rowAnnotations, entryName))
{
rowAnnotations.Add(entryName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Entry name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 1)) // Gene name
{
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <string> rowAnnotations = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
string geneName = entry.GeneName;
if (geneName != null && !ArrayUtils.Contains(rowAnnotations, geneName))
{
rowAnnotations.Add(geneName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Gene name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 2))
{
// Verbose protein name, i.e. all protein names annotated in all fasta headers, including the
//'Isoform x of...' prefixes and '(Fragment)' suffixes
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <string> rowAnnotations = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
string proteinName = entry.ProteinName;
if (proteinName != null && !ArrayUtils.Contains(rowAnnotations, proteinName))
{
rowAnnotations.Add(proteinName);
}
}
annotationColumn[row] = string.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Protein name (verbose)", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 3)) // Consensus protein name
{
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <string> rowAnnotations = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
string proteinName = entry.ConsensusProteinName;
if (proteinName != null && !ArrayUtils.Contains(rowAnnotations, proteinName))
{
rowAnnotations.Add(proteinName);
}
}
annotationColumn[row] = String.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Protein name", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 4)) // Species
{
string[] annotationColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <string> rowAnnotations = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
string speciesName = entry.Species;
if (speciesName != null && !ArrayUtils.Contains(rowAnnotations, speciesName))
{
rowAnnotations.Add(speciesName);
}
}
annotationColumn[row] = String.Join(";", rowAnnotations.ToArray());
}
mdata.AddStringColumn("Species", "", annotationColumn);
}
// Numeric annotations
processInfo.Status("Adding numeric annotations.");
selection =
param.GetParamWithSubParams <int>("Numeric annotations").GetSubParameters().GetParam <int[]>("Annotations").Value;
bool annotateLeadingId = param.GetParamWithSubParams <int>("Numeric annotations").Value == 1;
if (ArrayUtils.Contains(selection, 0)) // Sequence length
{
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <double> rowAnnotations = new List <double>();
foreach (ProteinSequence entry in fastaEntries[row])
{
double sequenceLength = entry.GetSequence().Length;
rowAnnotations.Add(sequenceLength);
if (annotateLeadingId && rowAnnotations.Count > 0)
{
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Sequence length", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 1)) // Monoisotopic molecular mass
{
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <double> rowAnnotations = new List <double>();
foreach (ProteinSequence entry in fastaEntries[row])
{
double monoisotopicMass = entry.GetMonoisotopicMolecularMass();
rowAnnotations.Add(monoisotopicMass);
if (annotateLeadingId && rowAnnotations.Count > 0)
{
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Monoisotopic molecular mass", "", annotationColumn);
}
if (ArrayUtils.Contains(selection, 2)) // Average molecular mass
{
double[] annotationColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <double> rowAnnotations = new List <double>();
foreach (ProteinSequence entry in fastaEntries[row])
{
double averageMass = entry.GetAverageMolecularMass();
rowAnnotations.Add(averageMass);
if (annotateLeadingId && rowAnnotations.Count > 0)
{
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
}
mdata.AddNumericColumn("Average molecular mass", "", annotationColumn);
}
// Theoretical peptides
processInfo.Status("Calculating theoretical peptides.");
annotateLeadingId = param.GetParamWithSubParams <int>("Calculate theoretical peptides").Value == 1;
Protease[] proteases = ArrayUtils.SubArray(Constants.defaultProteases,
param.GetParamWithSubParams <int>("Calculate theoretical peptides").GetSubParameters().GetParam <int[]>("Proteases")
.Value);
double minLength =
param.GetParamWithSubParams <int>("Calculate theoretical peptides").GetSubParameters().GetParam <double>(
"Min. peptide length").Value;
double maxLength =
param.GetParamWithSubParams <int>("Calculate theoretical peptides").GetSubParameters().GetParam <double>(
"Max. peptide length").Value;
bool displayPeptideSequences = annotateLeadingId &&
param.GetParamWithSubParams <int>("Calculate theoretical peptides").GetSubParameters().GetParam <bool>(
"Show sequences").Value;
foreach (Protease protease in proteases)
{
double[] annotationColumn = new double[mdata.RowCount];
string[] peptideColumn = new string[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <double> rowAnnotations = new List <double>();
List <string> rowPeptides = new List <string>();
foreach (ProteinSequence entry in fastaEntries[row])
{
double nTheoreticalPeptides = entry.GetNumberOfTheoreticalPeptides(protease, (int)minLength, (int)maxLength);
rowAnnotations.Add(nTheoreticalPeptides);
if (displayPeptideSequences)
{
rowPeptides.AddRange(entry.GetTheoreticalPeptideSequences(protease, (int)minLength, (int)maxLength));
}
if (annotateLeadingId && rowAnnotations.Count > 0)
{
break;
}
}
annotationColumn[row] = ArrayUtils.Median(rowAnnotations.ToArray());
peptideColumn[row] = String.Join(";", rowPeptides);
}
mdata.AddNumericColumn(
"Number of theoretical peptides (" + protease.name + ", " + minLength + "-" + maxLength + ")", "", annotationColumn);
if (displayPeptideSequences)
{
mdata.AddStringColumn(
"Theoretical peptide sequences (" + protease.name + ", " + minLength + "-" + maxLength + ")", "", peptideColumn);
}
}
// Sequence features
processInfo.Status("Counting sequence features.");
annotateLeadingId = param.GetParamWithSubParams <int>("Count sequence features").Value == 1;
bool normalizeBySequenceLength =
param.GetParamWithSubParams <int>("Count sequence features").GetSubParameters().GetParam <bool>(
"Normalize by sequence length").Value;
if (param.GetParamWithSubParams <int>("Count sequence features").GetSubParameters().GetParam <string>("Regex").Value !=
"")
{
Regex regex;
try{
regex =
new Regex(
param.GetParamWithSubParams <int>("Count sequence features").GetSubParameters().GetParam <string>("Regex").Value);
} catch (ArgumentException) {
processInfo.ErrString = "The regular expression you provided has invalid syntax.";
return;
}
double[] sequenceFeatureColumn = new double[mdata.RowCount];
for (int row = 0; row < mdata.RowCount; row++)
{
List <double> featureCount = new List <double>();
foreach (ProteinSequence entry in fastaEntries[row])
{
double nFeatures = regex.Matches(entry.GetSequence()).Count;
featureCount.Add(normalizeBySequenceLength ? nFeatures / entry.GetLength() : nFeatures);
if (annotateLeadingId)
{
break;
}
}
sequenceFeatureColumn[row] = ArrayUtils.Median(featureCount.ToArray());
}
mdata.AddNumericColumn(
(normalizeBySequenceLength ? "Normalized feature count (" : "Feature count (") + regex + ")", "",
sequenceFeatureColumn);
}
processInfo.Status("Done.");
}
public void LoadData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
int nrows = param.GetParam <int>("Number of rows").Value;
int ncols = param.GetParam <int>("Number of columns").Value;
int missingPerc = param.GetParam <int>("Percentage of missing values").Value;
int ngroups = param.GetParam <int>("Number of groups").Value;
ParameterWithSubParams <bool> setSeed = param.GetParamWithSubParams <bool>("Set seed");
Random2 randy = setSeed.Value? new Random2(setSeed.GetSubParameters().GetParam <int>("Seed").Value) : new Random2();
ngroups = Math.Min(ngroups, ncols);
float[,] m = new float[nrows, ncols];
ParameterWithSubParams <int> x = param.GetParamWithSubParams <int>("Mode");
Parameters subParams = x.GetSubParameters();
List <string> catColNames = new List <string>();
List <string[][]> catCols = new List <string[][]>();
switch (x.Value)
{
case 0:
for (int i = 0; i < m.GetLength(0); i++)
{
for (int j = 0; j < m.GetLength(1); j++)
{
if (randy.NextDouble() * 100 < missingPerc)
{
m[i, j] = float.NaN;
}
else
{
m[i, j] = (float)randy.NextGaussian();
}
}
}
break;
case 1:
float dist = (float)subParams.GetParam <double>("Distance").Value;
string[][] col = new string[m.GetLength(0)][];
for (int i = 0; i < m.GetLength(0); i++)
{
bool which = randy.NextDouble() < 0.5;
for (int j = 0; j < m.GetLength(1); j++)
{
if (randy.NextDouble() * 100 < missingPerc)
{
m[i, j] = float.NaN;
}
else
{
m[i, j] = (float)randy.NextGaussian();
}
}
if (which)
{
m[i, 0] += dist;
col[i] = new[] { "Group1" };
}
else
{
col[i] = new[] { "Group2" };
}
}
catColNames.Add("Grouping");
catCols.Add(col);
break;
case 2:
double boxLen = subParams.GetParam <double>("Box size").Value;
int howMany = subParams.GetParam <int>("How many").Value;
string[][] col1 = new string[m.GetLength(0)][];
float[,] centers = new float[howMany, m.GetLength(1)];
for (int i = 0; i < centers.GetLength(0); i++)
{
for (int j = 0; j < centers.GetLength(1); j++)
{
centers[i, j] = (float)(randy.NextDouble() * boxLen);
}
}
for (int i = 0; i < m.GetLength(0); i++)
{
int which = (int)(randy.NextDouble() * howMany);
for (int j = 0; j < m.GetLength(1); j++)
{
if (randy.NextDouble() * 100 < missingPerc)
{
m[i, j] = float.NaN;
}
else
{
m[i, j] = (float)randy.NextGaussian() + centers[which, j];
}
}
col1[i] = new[] { "Group" + (which + 1) };
}
catColNames.Add("Grouping");
catCols.Add(col1);
break;
}
List <string> exprColumnNames = new List <string>();
for (int i = 0; i < ncols; i++)
{
exprColumnNames.Add("Column " + (i + 1));
}
mdata.Name = "Random matrix";
mdata.ColumnNames = exprColumnNames;
mdata.Values.Set(m);
mdata.Quality.Set(new float[m.GetLength(0), m.GetLength(1)]);
mdata.IsImputed.Set(new bool[m.GetLength(0), m.GetLength(1)]);
mdata.SetAnnotationColumns(new List <string>(), new List <string[]>(), catColNames, catCols, new List <string>(),
new List <double[]>(), new List <string>(), new List <double[][]>());
mdata.Origin = "Random matrix";
string[] names = new string[mdata.RowCount];
for (int i = 0; i < names.Length; i++)
{
names[i] = "Row " + (i + 1);
}
mdata.AddStringColumn("Name", "Name", names);
string[][] grouping = new string[ncols][];
for (int i = 0; i < ncols; i++)
{
int ig = (i * ngroups) / ncols + 1;
grouping[i] = new[] { "Group" + ig };
}
mdata.AddCategoryRow("Grouping", "Grouping", grouping);
}
