public UniprotParser(string swissprotFileName, string tremblFileName, bool includeTrembl, HandleUniprotEntry handle)
{
if (swissprotFileName != null){
this.swissprotFileName = swissprotFileName;
}
if (tremblFileName != null){
this.tremblFileName = tremblFileName;
}
Parse(this.swissprotFileName, handle, false);
if (includeTrembl){
Parse(this.tremblFileName, handle, true);
}
}
private void Parse(string filename, HandleUniprotEntry handle, bool isTrembl)
{
Stream fileStream = new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read);
Stream stream = filename.ToLower().EndsWith(".gz")
? new GZipStream(fileStream, CompressionMode.Decompress) : fileStream;
XmlTextReader reader = new XmlTextReader(new StreamReader(stream));
while (reader.Read())
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
string name = reader.Name;
Dictionary <string, string> attributes = new Dictionary <string, string>();
if (reader.HasAttributes)
{
for (int i = 0; i < reader.AttributeCount; i++)
{
reader.MoveToAttribute(i);
attributes.Add(reader.Name, reader.Value);
}
}
StartElement(name, attributes);
level++;
break;
case XmlNodeType.EndElement:
level--;
EndElement(reader.Name, handle, isTrembl);
break;
case XmlNodeType.Text:
Characters(reader.Value, 0, reader.Value.Length);
break;
}
}
}
private void Parse(string filename, HandleUniprotEntry handle, bool isTrembl)
{
Stream fileStream = new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read);
Stream stream = filename.ToLower().EndsWith(".gz")
? new GZipStream(fileStream, CompressionMode.Decompress) : fileStream;
XmlTextReader reader = new XmlTextReader(new StreamReader(stream));
while (reader.Read()){
switch (reader.NodeType){
case XmlNodeType.Element:
string name = reader.Name;
Dictionary<string, string> attributes = new Dictionary<string, string>();
if (reader.HasAttributes){
for (int i = 0; i < reader.AttributeCount; i++){
reader.MoveToAttribute(i);
attributes.Add(reader.Name, reader.Value);
}
}
StartElement(name, attributes);
level++;
break;
case XmlNodeType.EndElement:
level--;
EndElement(reader.Name, handle, isTrembl);
break;
case XmlNodeType.Text:
Characters(reader.Value, 0, reader.Value.Length);
break;
}
}
}
private void EndElement(IEquatable<string> qName, HandleUniprotEntry handle, bool isTrembl)
{
if (qName.Equals("sequence")){
entry.Sequence = StringUtils.RemoveWhitespace(sequence.ToString());
sequence = null;
} else if (qName.Equals("keyword")) {
entry.AddKeyword(StringUtils.RemoveWhitespace(keyword.ToString()));
keyword = null;
} else if (qName.Equals("molecule") && dbReferenceType.Equals("Ensembl")){
string mol = molecule.ToString().Trim();
entry.AddDbEntryProperty(dbReferenceType, dbReferenceId, "isoform ID", mol);
if (!isoformToEnst.ContainsKey(mol))
isoformToEnst.Add(mol, new List<string>());
isoformToEnst[mol].Add(dbReferenceId);
molecule = null;
} else if (qName.Equals("entry")){
entry.Accessions = accessions.ToArray();
entry.ProteinFullNames = proteinFullNames.ToArray();
entry.ProteinShortNames = proteinShortNames.ToArray();
entry.ProteinEcNumbers = proteinEcNumbers.ToArray();
entry.GeneNamesAndTypes = gnames.ToArray();
entry.OrganismNames = onames.ToArray();
entry.UniprotNames = unames.ToArray();
entry.IsTrembl = isTrembl;
if (resolveIsoforms){
if (numIsoforms > 1 && isoformToEnst.Count > 1){
List<UniprotEntry> isoEntries = entry.ResolveIsoforms(isoformToEnst);
foreach (UniprotEntry e in isoEntries){
handle(e);
}
} else
handle(entry);
} else
handle(entry);
} else if (qName.Equals("dbReference")){
inDbRef = false;
} else if (qName.Equals("accession")){
accessions.Add(StringUtils.RemoveWhitespace(accession.ToString()));
accession = null;
} else if (qName.Equals("location")){
if (inFeature){
//inFeatureLocation = false;
entry.AddFeatureLocation(featureBegin, featureEnd);
}
} else if (qName.Equals("variation")){
if (inFeature){
entry.AddFeatureVariation(StringUtils.RemoveWhitespace(variation.ToString()));
variation = null;
}
} else if (qName.Equals("original")){
if (inFeature){
entry.AddFeatureOriginal(StringUtils.RemoveWhitespace(original.ToString()));
original = null;
}
} else if (qName.Equals("feature")){
inFeature = false;
foreach (FeatureType type in entry.GetAllFeatureTypes()){
int c = entry.GetFeatureCount(type);
if (!featureCounts.ContainsKey(type)){
featureCounts.Add(type, 0);
}
featureCounts[type] += c;
}
} else if (qName.Equals("fullName") && inProteinRecommendedName){
proteinFullNames.Add(proteinFullName.ToString().Trim());
proteinFullName = null;
} else if (qName.Equals("shortName") && inProteinRecommendedName){
proteinShortNames.Add(proteinShortName.ToString().Trim());
proteinShortName = null;
} else if (qName.Equals("ecNumber") && inProteinRecommendedName){
proteinEcNumbers.Add(proteinEcNumber.ToString().Trim());
proteinEcNumber = null;
} else if (qName.Equals("name") && inGene){
gnames.Add(new Tuple<string, string>(gname.ToString().Trim(), gnameType.Trim()));
gname = null;
gnameType = null;
} else if (qName.Equals("name") && inOrganism){
string on = oname?.ToString().Trim();
if (@on?.Length > 0){
onames.Add(@on);
oname = null;
}
} else if (qName.Equals("name") && level == 1){
unames.Add(uname.ToString().Trim());
uname = null;
} else if (qName.Equals("protein")){
inProtein = false;
} else if (qName.Equals("recommendedName") && inProtein){
inProteinRecommendedName = false;
} else if (qName.Equals("gene")){
inGene = false;
} else if (qName.Equals("organism")) {
inOrganism = false;
} else if (qName.Equals("organismHost")) {
inOrganismHost = false;
}
}
private void EndElement(IEquatable<string> qName, HandleUniprotEntry handle, bool isTrembl)
{
if (qName.Equals("sequence")){
entry.Sequence = StringUtils.RemoveWhitespace(sequence.ToString());
sequence = null;
} else if (qName.Equals("keyword")) {
entry.AddKeyword(StringUtils.RemoveWhitespace(keyword.ToString()));
keyword = null;
} else if (qName.Equals("entry")) {
entry.Accessions = accessions.ToArray();
entry.ProteinFullNames = proteinFullNames.ToArray();
entry.ProteinShortNames = proteinShortNames.ToArray();
entry.ProteinEcNumbers = proteinEcNumbers.ToArray();
entry.GeneNamesAndTypes = gnames.ToArray();
entry.OrganismNames = onames.ToArray();
entry.UniprotNames = unames.ToArray();
entry.IsTrembl = isTrembl;
handle(entry);
entryCount++;
} else if (qName.Equals("dbReference")){
inDbRef = false;
} else if (qName.Equals("accession")){
accessions.Add(StringUtils.RemoveWhitespace(accession.ToString()));
accession = null;
} else if (qName.Equals("location")){
if (inFeature){
inFeatureLocation = false;
entry.AddFeatureLocation(featureBegin, featureEnd);
}
} else if (qName.Equals("variation")){
if (inFeature){
entry.AddFeatureVariation(StringUtils.RemoveWhitespace(variation.ToString()));
variation = null;
}
} else if (qName.Equals("original")){
if (inFeature){
entry.AddFeatureOriginal(StringUtils.RemoveWhitespace(original.ToString()));
original = null;
}
} else if (qName.Equals("feature")){
inFeature = false;
foreach (FeatureType type in entry.GetAllFeatureTypes()){
int c = entry.GetFeatureCount(type);
if (!featureCounts.ContainsKey(type)){
featureCounts.Add(type, 0);
}
featureCounts[type] += c;
}
} else if (qName.Equals("fullName") && inProteinRecommendedName){
proteinFullNames.Add(proteinFullName.ToString().Trim());
proteinFullName = null;
} else if (qName.Equals("shortName") && inProteinRecommendedName){
proteinShortNames.Add(proteinShortName.ToString().Trim());
proteinShortName = null;
} else if (qName.Equals("ecNumber") && inProteinRecommendedName){
proteinEcNumbers.Add(proteinEcNumber.ToString().Trim());
proteinEcNumber = null;
} else if (qName.Equals("name") && inGene){
gnames.Add(new Tuple<string, string>(gname.ToString().Trim(), gnameType.Trim()));
gname = null;
gnameType = null;
} else if (qName.Equals("name") && inOrganism){
if (oname != null){
string on = oname.ToString().Trim();
if (on.Length > 0){
onames.Add(on);
oname = null;
}
}
} else if (qName.Equals("name") && level == 1){
unames.Add(uname.ToString().Trim());
uname = null;
} else if (qName.Equals("protein")){
inProtein = false;
} else if (qName.Equals("recommendedName") && inProtein){
inProteinRecommendedName = false;
} else if (qName.Equals("gene")){
inGene = false;
} else if (qName.Equals("organism")) {
inOrganism = false;
} else if (qName.Equals("organismHost")) {
inOrganismHost = false;
}
}
public UniprotParser(string swissprotFileName, string tremblFileName, bool includeTrembl, HandleUniprotEntry handle, bool resolveIsos)
{
resolveIsoforms = resolveIsos;
if (swissprotFileName != null)
{
this.swissprotFileName = swissprotFileName;
}
if (tremblFileName != null)
{
this.tremblFileName = tremblFileName;
}
Parse(this.swissprotFileName, handle, false);
if (includeTrembl)
{
Parse(this.tremblFileName, handle, true);
}
}
private void EndElement(IEquatable <string> qName, HandleUniprotEntry handle, bool isTrembl)
{
if (qName.Equals("sequence"))
{
entry.Sequence = StringUtils.RemoveWhitespace(sequence.ToString());
sequence = null;
}
else if (qName.Equals("keyword"))
{
entry.AddKeyword(StringUtils.RemoveWhitespace(keyword.ToString()));
keyword = null;
}
else if (qName.Equals("molecule") && dbReferenceType.Equals("Ensembl"))
{
string mol = molecule.ToString().Trim();
entry.AddDbEntryProperty(dbReferenceType, dbReferenceId, "isoform ID", mol);
if (!isoformToEnst.ContainsKey(mol))
{
isoformToEnst.Add(mol, new List <string>());
}
isoformToEnst[mol].Add(dbReferenceId);
molecule = null;
}
else if (qName.Equals("entry"))
{
entry.Accessions = accessions.ToArray();
entry.ProteinFullNames = proteinFullNames.ToArray();
entry.ProteinShortNames = proteinShortNames.ToArray();
entry.ProteinEcNumbers = proteinEcNumbers.ToArray();
entry.GeneNamesAndTypes = gnames.ToArray();
entry.OrganismNames = onames.ToArray();
entry.UniprotNames = unames.ToArray();
entry.IsTrembl = isTrembl;
if (resolveIsoforms)
{
if (numIsoforms > 1 && isoformToEnst.Count > 1)
{
List <UniprotEntry> isoEntries = entry.ResolveIsoforms(isoformToEnst);
foreach (UniprotEntry e in isoEntries)
{
handle(e);
}
}
else
{
handle(entry);
}
}
else
{
handle(entry);
}
}
else if (qName.Equals("dbReference"))
{
inDbRef = false;
}
else if (qName.Equals("accession"))
{
accessions.Add(StringUtils.RemoveWhitespace(accession.ToString()));
accession = null;
}
else if (qName.Equals("location"))
{
if (inFeature)
{
//inFeatureLocation = false;
entry.AddFeatureLocation(featureBegin, featureEnd);
}
}
else if (qName.Equals("variation"))
{
if (inFeature)
{
entry.AddFeatureVariation(StringUtils.RemoveWhitespace(variation.ToString()));
variation = null;
}
}
else if (qName.Equals("original"))
{
if (inFeature)
{
entry.AddFeatureOriginal(StringUtils.RemoveWhitespace(original.ToString()));
original = null;
}
}
else if (qName.Equals("feature"))
{
inFeature = false;
foreach (FeatureType type in entry.GetAllFeatureTypes())
{
int c = entry.GetFeatureCount(type);
if (!featureCounts.ContainsKey(type))
{
featureCounts.Add(type, 0);
}
featureCounts[type] += c;
}
}
else if (qName.Equals("fullName") && inProteinRecommendedName)
{
proteinFullNames.Add(proteinFullName.ToString().Trim());
proteinFullName = null;
}
else if (qName.Equals("shortName") && inProteinRecommendedName)
{
proteinShortNames.Add(proteinShortName.ToString().Trim());
proteinShortName = null;
}
else if (qName.Equals("ecNumber") && inProteinRecommendedName)
{
proteinEcNumbers.Add(proteinEcNumber.ToString().Trim());
proteinEcNumber = null;
}
else if (qName.Equals("name") && inGene)
{
gnames.Add(new Tuple <string, string>(gname.ToString().Trim(), gnameType.Trim()));
gname = null;
gnameType = null;
}
else if (qName.Equals("name") && inOrganism)
{
string on = oname?.ToString().Trim();
if (@on?.Length > 0)
{
onames.Add(@on);
oname = null;
}
}
else if (qName.Equals("name") && level == 1)
{
unames.Add(uname.ToString().Trim());
uname = null;
}
else if (qName.Equals("protein"))
{
inProtein = false;
}
else if (qName.Equals("recommendedName") && inProtein)
{
inProteinRecommendedName = false;
}
else if (qName.Equals("gene"))
{
inGene = false;
}
else if (qName.Equals("organism"))
{
inOrganism = false;
}
else if (qName.Equals("organismHost"))
{
inOrganismHost = false;
}
}
private void EndElement(IEquatable <string> qName, HandleUniprotEntry handle, bool isTrembl)
{
if (qName.Equals("sequence"))
{
entry.Sequence = StringUtils.RemoveWhitespace(sequence.ToString());
sequence = null;
}
else if (qName.Equals("keyword"))
{
entry.AddKeyword(StringUtils.RemoveWhitespace(keyword.ToString()));
keyword = null;
}
else if (qName.Equals("entry"))
{
entry.Accessions = accessions.ToArray();
entry.ProteinFullNames = proteinFullNames.ToArray();
entry.ProteinShortNames = proteinShortNames.ToArray();
entry.ProteinEcNumbers = proteinEcNumbers.ToArray();
entry.GeneNamesAndTypes = gnames.ToArray();
entry.OrganismNames = onames.ToArray();
entry.UniprotNames = unames.ToArray();
entry.IsTrembl = isTrembl;
handle(entry);
entryCount++;
}
else if (qName.Equals("dbReference"))
{
inDbRef = false;
}
else if (qName.Equals("accession"))
{
accessions.Add(StringUtils.RemoveWhitespace(accession.ToString()));
accession = null;
}
else if (qName.Equals("location"))
{
if (inFeature)
{
inFeatureLocation = false;
entry.AddFeatureLocation(featureBegin, featureEnd);
}
}
else if (qName.Equals("variation"))
{
if (inFeature)
{
entry.AddFeatureVariation(StringUtils.RemoveWhitespace(variation.ToString()));
variation = null;
}
}
else if (qName.Equals("original"))
{
if (inFeature)
{
entry.AddFeatureOriginal(StringUtils.RemoveWhitespace(original.ToString()));
original = null;
}
}
else if (qName.Equals("feature"))
{
inFeature = false;
foreach (FeatureType type in entry.GetAllFeatureTypes())
{
int c = entry.GetFeatureCount(type);
if (!featureCounts.ContainsKey(type))
{
featureCounts.Add(type, 0);
}
featureCounts[type] += c;
}
}
else if (qName.Equals("fullName") && inProteinRecommendedName)
{
proteinFullNames.Add(proteinFullName.ToString().Trim());
proteinFullName = null;
}
else if (qName.Equals("shortName") && inProteinRecommendedName)
{
proteinShortNames.Add(proteinShortName.ToString().Trim());
proteinShortName = null;
}
else if (qName.Equals("ecNumber") && inProteinRecommendedName)
{
proteinEcNumbers.Add(proteinEcNumber.ToString().Trim());
proteinEcNumber = null;
}
else if (qName.Equals("name") && inGene)
{
gnames.Add(new Tuple <string, string>(gname.ToString().Trim(), gnameType.Trim()));
gname = null;
gnameType = null;
}
else if (qName.Equals("name") && inOrganism)
{
if (oname != null)
{
string on = oname.ToString().Trim();
if (on.Length > 0)
{
onames.Add(on);
oname = null;
}
}
}
else if (qName.Equals("name") && level == 1)
{
unames.Add(uname.ToString().Trim());
uname = null;
}
else if (qName.Equals("protein"))
{
inProtein = false;
}
else if (qName.Equals("recommendedName") && inProtein)
{
inProteinRecommendedName = false;
}
else if (qName.Equals("gene"))
{
inGene = false;
}
else if (qName.Equals("organism"))
{
inOrganism = false;
}
else if (qName.Equals("organismHost"))
{
inOrganismHost = false;
}
}
