public IEnumerable <ITestCaseData> Tag_TestCases()
{
var tags = new HashSet <string> {
"Foo", "Bar", "Baz"
};
var standardAlphabetWithTags = new ProteinSequence("ACTCTTCAGC", AlphabetType.StandardProtein, GeneticCode.Standard, tags);
yield return(new TestCaseData(standardAlphabetWithTags, tags).SetName("Standard protein alphabet with tags"));
var extendedAlphabetWithTags = new ProteinSequence("AUCUAGCGCGUA", AlphabetType.ExtendedProtein, GeneticCode.Standard, tags);
yield return(new TestCaseData(extendedAlphabetWithTags, tags).SetName("Extended protein alphabet with tags"));
}
public IEnumerable <ITestCaseData> Equality_TestCases()
{
const string standard = "ACTGC";
const string extended = "ACUGC";
var standardStandard = new ProteinSequence(standard, AlphabetType.StandardProtein, GeneticCode.Standard);
var standardExtended = new ProteinSequence(standard, AlphabetType.ExtendedProtein, GeneticCode.Standard);
var extendedExtended = new ProteinSequence(extended, AlphabetType.ExtendedProtein, GeneticCode.Standard);
var standardDiffStandard = new ProteinSequence(standard.Substring(0, standard.Length - 2), AlphabetType.StandardProtein, GeneticCode.Standard);
var extendedDiffExtended = new ProteinSequence(extended.Substring(0, extended.Length - 2), AlphabetType.ExtendedProtein, GeneticCode.Standard);
yield return(new TestCaseData(standardStandard, standardStandard).Returns(true).SetName("Standard with standard"));
yield return(new TestCaseData(standardStandard, standardExtended).Returns(false).SetName("Standard with extended protein returns false"));
yield return(new TestCaseData(standardStandard, standardDiffStandard).Returns(false).SetName("Two different standard protein sequences return false"));
yield return(new TestCaseData(extendedExtended, extendedDiffExtended).Returns(false).SetName("Two different extended protein sequences return false"));
}
public void ParseFile(string path, ProcessInfo processInfo)
{
processInfo.Status("Parsing " + path);
string accession = "";
int sequenceCounter = 0;
StringBuilder sequence = new StringBuilder();
ProteinSequence protein = new ProteinSequence();
try{
StreamReader file = new StreamReader(path);
string line;
while ((line = file.ReadLine()) != null){ // valid line
if (sequenceCounter%500 == 0){
processInfo.Status("Parsing " + path + ", " + (int) ((float) file.BaseStream.Position/file.BaseStream.Length*100) +
"%");
}
bool lineIsHeader = line.StartsWith(">");
// skip all lines until the first header is found
if (sequenceCounter == 0 && !lineIsHeader){
continue;
}
// line is a piece of a sequence
if (sequenceCounter > 0 && !lineIsHeader){
sequence.Append(line.Trim());
continue;
}
// line is a fasta header
if (lineIsHeader){
if (sequenceCounter > 0)
// this is not the first header, i.e. the previous sequence is now completely read in
{
// add the previous protein
protein.SetSequence(sequence.ToString());
entries.Add(accession, protein);
}
// initialize a new protein
protein = new ProteinSequence();
sequenceCounter++;
// then parse the new header
string header = line;
Match m = regexUniprotAccession.Match(header);
if (m.Success){ // uniprot header
accession = m.Groups[1].Value;
protein.Accession = accession;
protein.Header = header;
} else{ // fallback position: take entire header after the > as accession
accession = header.Substring(1).Trim();
protein.Accession = accession;
protein.Header = header;
}
sequence = new StringBuilder();
}
} //end while
file.Close();
//add the last protein
if (sequenceCounter > 0){ // make sure there is at least one sequence in the file
protein.SetSequence(sequence.ToString());
entries.Add(accession, protein);
}
} catch (Exception){
processInfo.ErrString =
"Something went wrong while parsing the fasta file.\nMake sure the path is correct and the " +
"file is not opened in another application.\nMake sure the fasta file is valid.";
}
}
public ProteinSequenceMatchDuo(ProteinSequence proteinSequence, ProteinMatch proteinMatch)
{
ProteinSequence = proteinSequence;
ProteinMatch = proteinMatch;
}
public void Tag_Tests(ProteinSequence incoming, IEnumerable <string> incomingTags)
{
var expected = new HashSet <string>(incomingTags);
CollectionAssert.AreEquivalent(incoming.Tags, expected);
}
public int Constructor_Tests(string sequence, AlphabetType alphabet)
{
var protein = new ProteinSequence(sequence, alphabet, GeneticCode.Standard);
return(protein.Sequence.Length);
}
public bool EqualityTests(ProteinSequence a, ProteinSequence b)
{
return(a.Equals(b));
}
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.");
}
