/// <summary>
/// Private Constructor for clone method.
/// </summary>
/// <param name="other">GenBankMetadata instance to clone.</param>
private GenBankMetadata(GenBankMetadata other)
{
if (other.Locus != null)
{
Locus = other.Locus.Clone();
}
Definition = other.Definition;
if (other.Accession != null)
{
Accession = other.Accession.Clone();
}
if (other.Version != null)
{
Version = other.Version.Clone();
}
if (other.Project != null)
{
Project = other.Project.Clone();
}
if (other.DbLinks != null)
{
DbLinks = other.DbLinks.ToList();
}
DbSource = other.DbSource;
Keywords = other.Keywords;
if (other.Segment != null)
{
Segment = other.Segment.Clone();
}
if (other.Source != null)
{
Source = other.Source.Clone();
}
References = new List<CitationReference>();
foreach (CitationReference reference in other.References)
{
References.Add(reference.Clone());
}
Comments = new List<string>(other.Comments);
Primary = other.Primary;
if (other.Features != null)
{
Features = other.Features.Clone();
}
BaseCount = other.BaseCount;
Origin = other.Origin;
Contig = other.Contig;
}
// Write all the header sections that come before the features section.
private void WriteHeaders(ISequence sequence, TextWriter txtWriter)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
if (metadata != null)
{
WriteLocus(sequence, txtWriter);
WriteHeaderSection("DEFINITION", metadata.Definition, txtWriter);
if (metadata.Accession != null)
{
WriteHeaderSection("ACCESSION", Helper.GetGenBankAccession(metadata.Accession), txtWriter);
string version;
if (metadata.Version != null)
{
version = metadata.Accession.Primary + "." + metadata.Version.Version;
if (!string.IsNullOrEmpty(metadata.Version.GiNumber))
{
version += " GI:" + metadata.Version.GiNumber;
}
if (version.Length > 0)
{
WriteHeaderSection("VERSION", version, txtWriter);
}
}
}
if (metadata.Project != null)
{
WriteHeaderSection("PROJECT", Helper.GetProjectIdentifier(metadata.Project), txtWriter);
}
if (metadata.DbLinks != null && metadata.DbLinks.Count > 0)
{
WriteHeaderSection("DBLINK", Helper.GetCrossReferenceLink(metadata.DbLinks), txtWriter);
}
WriteHeaderSection("DBSOURCE", metadata.DbSource, txtWriter);
WriteHeaderSection("KEYWORDS", metadata.Keywords, txtWriter);
if (metadata.Segment != null)
{
WriteHeaderSection("SEGMENT", Helper.GetSequenceSegment(metadata.Segment), txtWriter);
}
WriteSource(metadata, txtWriter);
WriteReferences(metadata, txtWriter);
WriteComments(metadata, txtWriter);
WriteHeaderSection("PRIMARY", metadata.Primary, txtWriter);
}
}
private void WriteFeatures(ISequence sequence, TextWriter txtWriter)
{
ILocationBuilder locBuilder = LocationBuilder;
if (locBuilder == null)
{
throw new InvalidOperationException(Properties.Resource.NullLocationBuild);
}
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
if (metadata != null && metadata.Features != null)
{
WriteFeatureSection("FEATURES", "Location/Qualifiers", txtWriter);
// write the features in the order they were put in the list
foreach (FeatureItem feature in metadata.Features.All)
{
WriteFeatureSection(FeatureHeaderIndentString + feature.Key, locBuilder.GetLocationString(feature.Location), txtWriter);
// The sub-items of a feature are referred to as qualifiers. These do not have
// unique keys, so they are stored as lists in the SubItems dictionary.
foreach (KeyValuePair <string, List <string> > qualifierList in feature.Qualifiers)
{
foreach (string qualifierValue in qualifierList.Value)
{
string data = "/" + qualifierList.Key;
if (qualifierValue != null)
{
if (qualifierValue != string.Empty)
{
data += "=";
string s = "" + (char)34;
if (qualifierValue.StartsWith(s) == false)
{
data += s;
}
data += qualifierValue;
if (qualifierValue.EndsWith(s) == false)
{
data += s;
}
}
}
// use a blank header; the qualifier key is part of the data
WriteFeatureSection(string.Empty, data, txtWriter);
}
}
}
}
}
/// <summary>
/// Parses the GenBank Sequence from the GenBank file.
/// Handle optional BASE COUNT, then ORIGIN and sequence data.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="sequence">The sequence.</param>
/// <param name="stream">The stream reader.</param>
private void ParseSequence(ref string line, ref Sequence sequence, StreamReader stream)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
while (line != null)
{
if (line.StartsWith("//", StringComparison.Ordinal))
{
line = GoToNextLine(line, stream);
break;
// end of sequence record
}
// set data indent for sequence headers
string lineHeader = GetLineHeader(line, DataIndent);
switch (lineHeader)
{
case "BASE COUNT":
// The BASE COUNT linetype is obsolete and was removed
// from the GenBank flat-file format in October 2003. But if it is
// present, we will use it. We get the untrimmed version since it
// starts with a right justified column.
metadata.BaseCount = line.Substring(DataIndent);
line = GoToNextLine(line, stream);
break;
case "ORIGIN":
// Change Note: The original implementation would validate the alphabet every line
// which would greatly impact performance on large sequences. This updates the method
// to improve performance by validating the alphabet after parsing the sequence.
ParseOrigin(ref line, metadata, stream);
break;
case "CONTIG":
metadata.Contig = ParseMultiLineData(ref line, Environment.NewLine, DataIndent, stream);
// don't go to next line; current line still needs to be processed
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserUnexpectedLineInSequence,
line);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
}
/// <summary>
/// Extracts supposed sequence name from metadata.
/// </summary>
/// <param name="metadata">
/// The metadata.
/// </param>
/// <returns>
/// Supposed name as <see cref="string"/>.
/// </returns>
/// <exception cref="Exception">
/// Thrown if all name fields are contradictory.
/// </exception>
public static string ExtractSequenceName(GenBankMetadata metadata)
{
string species = metadata.Source.Organism.Species.GetLargestRepeatingSubstring();
string commonName = metadata.Source.CommonName;
string definition = metadata.Definition.TrimEnd(", complete genome.")
.TrimEnd(", complete sequence.")
.TrimEnd(", complete CDS.")
.TrimEnd(", complete cds.")
.TrimEnd(", genome.");
if (commonName.Contains(species))
{
if (definition.Contains(commonName))
{
return definition;
}
if (commonName.Contains(definition))
{
return commonName;
}
return commonName + " | " + definition;
}
if (species.Contains(commonName))
{
if (definition.Contains(species))
{
return definition;
}
if (species.Contains(definition))
{
return species;
}
return species + " | " + definition;
}
throw new Exception("Sequences names are not equal. CommonName = " + commonName +
", Species = " + species +
", Definition = " + definition);
}
private void WriteReferences(GenBankMetadata metadata, TextWriter txtWriter)
{
if (metadata.References != null)
{
foreach (CitationReference reference in metadata.References)
{
// format the data for the first line
string data = reference.Number.ToString(CultureInfo.InvariantCulture);
if (!string.IsNullOrEmpty(reference.Location))
{
data = data.PadRight(3) + "(" + reference.Location + ")";
}
WriteHeaderSection("REFERENCE", data, txtWriter);
WriteHeaderSection(" AUTHORS", reference.Authors, txtWriter);
WriteHeaderSection(" CONSRTM", reference.Consortiums, txtWriter);
WriteHeaderSection(" TITLE", reference.Title, txtWriter);
WriteHeaderSection(" JOURNAL", reference.Journal, txtWriter);
WriteHeaderSection(" MEDLINE", reference.Medline, txtWriter);
WriteHeaderSection(" PUBMED", reference.PubMed, txtWriter);
WriteHeaderSection(" REMARK", reference.Remarks, txtWriter);
}
}
}
/// <summary>
/// Extracts sequence feature.
/// </summary>
/// <param name="metadata">
/// The metadata.
/// </param>
/// <returns>
/// The <see cref="int"/>.
/// </returns>
public int ExtractSequenceFeature(GenBankMetadata metadata)
{
string name = metadata.Definition.ToLower();
if (name.Contains("mitochondrion"))
{
return Aliases.Feature.MitochondrionGenome;
}
else if (name.Contains("chloroplast"))
{
return Aliases.Feature.ChloroplastGenome;
}
else if (name.Contains("plasmid"))
{
return Aliases.Feature.Plasmid;
}
else if (name.Contains("plastid"))
{
return Aliases.Feature.Plastid;
}
else
{
return Aliases.Feature.FullGenome;
}
}
/// <summary>
/// Validate TrnsitPeptide features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankTrnsitPeptideFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<TransitPeptide> tansitPeptideFeatureList =
genMetadata.Features.TransitPeptides;
var locBuilder = new LocationBuilder();
// Create a copy of transit peptide features.
TransitPeptide cloneTransit = tansitPeptideFeatureList[0].Clone();
// Validate transit peptide qualifiers.
Assert.AreEqual(tansitPeptideFeatureList.Count.ToString((IFormatProvider) null), featureCount);
Assert.AreEqual(cloneTransit.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneTransit.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(tansitPeptideFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(tansitPeptideFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(tansitPeptideFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(tansitPeptideFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(tansitPeptideFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(tansitPeptideFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(tansitPeptideFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.TransitPeptides[0].Location),
expectedLocation);
Assert.AreEqual(tansitPeptideFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(tansitPeptideFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(tansitPeptideFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(tansitPeptideFeatureList[0].Function[0],
expectedFunction);
// Create a new TransitPeptide and validate the same.
var tPeptide = new TransitPeptide(expectedLocation);
var tPeptideWithILoc = new TransitPeptide(
genMetadata.Features.TransitPeptides[0].Location);
// Set qualifiers and validate them.
tPeptide.Allele = expectedAllele;
tPeptide.GeneSymbol = geneSymbol;
tPeptideWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(tPeptide.GeneSymbol, geneSymbol);
Assert.AreEqual(tPeptide.Allele, expectedAllele);
Assert.AreEqual(tPeptideWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Parses reference info.
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseReference(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string Key;
string subKey;
string value;
string message;
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
rowIndex++;
CitationReference reference = new CitationReference();
if (!string.IsNullOrWhiteSpace(value))
{
// check for start/end e.g. (bases 1 to 118), or prose notes
Match m = Regex.Match(value,
@"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (m.Success)
{
// create new reference
string number = m.Groups["number"].Value;
string location = m.Groups["location"].Value;
int outValue;
if (!int.TryParse(number, out outValue))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
reference.Number = outValue;
reference.Location = location;
}
}
while (rowIndex < cellRange.GetLength(0))
{
if (3 > cellRange.GetLength(1))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
if (null != cellRange[rowIndex, KeyColumnIndex])
{
Key = cellRange[rowIndex, KeyColumnIndex].ToString();
if (!string.IsNullOrWhiteSpace(Key))
{
break;
}
}
if (null == cellRange[rowIndex, SubKeyColumnIndex] || string.IsNullOrWhiteSpace(cellRange[rowIndex, SubKeyColumnIndex].ToString()))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
subKey = cellRange[rowIndex, SubKeyColumnIndex].ToString().ToUpperInvariant();
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
if (string.IsNullOrWhiteSpace(value))
{
continue;
}
switch (subKey)
{
case REFERENCE_AUTHORS:
reference.Authors = value;
break;
case REFERENCE_CONSORTIUMS:
reference.Consortiums = value;
break;
case REFERENCE_JOURNAL:
reference.Journal = value;
break;
case REFERENCE_MEDLINE:
reference.Medline = value;
break;
case REFERENCE_PUBMED:
reference.PubMed = value;
break;
case REFERENCE_REMARK:
reference.Remarks = value;
break;
case REFERENCE_TITLE:
reference.Title = value;
break;
}
rowIndex++;
}
metadata.References.Add(reference);
return rowIndex;
}
/// <summary>
/// Parses locus info.
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseLocus(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string Key;
string subKey;
string value;
string message;
rowIndex++;
while (rowIndex < cellRange.GetLength(0))
{
if (3 > cellRange.GetLength(1))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS);
throw new FormatException(message);
}
if (null != cellRange[rowIndex, KeyColumnIndex])
{
Key = cellRange[rowIndex, KeyColumnIndex].ToString();
if (!string.IsNullOrWhiteSpace(Key))
{
break;
}
}
if (null == cellRange[rowIndex, SubKeyColumnIndex] || string.IsNullOrWhiteSpace(cellRange[rowIndex, SubKeyColumnIndex].ToString()))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS);
throw new FormatException(message);
}
if (metadata.Locus == null)
{
metadata.Locus = new GenBankLocusInfo();
}
subKey = cellRange[rowIndex, SubKeyColumnIndex].ToString().ToUpperInvariant();
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
switch (subKey)
{
case LOCUS_NAME:
metadata.Locus.Name = value;
break;
case LOCUS_SEQLEN:
if (!string.IsNullOrWhiteSpace(value))
{
metadata.Locus.SequenceLength = int.Parse(value);
}
break;
case LOCUS_SEQTYPE:
metadata.Locus.SequenceType = value;
break;
case LOCUS_MOLTYPE:
MoleculeType moleculetype = MoleculeType.NA;
if (!string.IsNullOrWhiteSpace(value) && Enum.TryParse<MoleculeType>(value, true, out moleculetype))
{
metadata.Locus.MoleculeType = moleculetype;
}
else
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS_MOLTYPE);
throw new FormatException(message);
}
break;
case LOCUS_STRANTTOPOLOGY:
SequenceStrandTopology strandTopology = SequenceStrandTopology.None;
if (!string.IsNullOrWhiteSpace(value) && Enum.TryParse<SequenceStrandTopology>(value, true, out strandTopology))
{
metadata.Locus.StrandTopology = strandTopology;
}
else
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS_STRANTTOPOLOGY);
throw new FormatException(message);
}
break;
case LOCUS_STRANDTYPE:
SequenceStrandType strandtype = SequenceStrandType.None;
if (!string.IsNullOrWhiteSpace(value) && Enum.TryParse<SequenceStrandType>(value, true, out strandtype))
{
metadata.Locus.Strand = strandtype;
}
else
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS_STRANDTYPE);
throw new FormatException(message);
}
break;
case LOCUS_DIVISIONCODE:
SequenceDivisionCode divisionCode = SequenceDivisionCode.None;
if (!string.IsNullOrWhiteSpace(value) && Enum.TryParse<SequenceDivisionCode>(value, true, out divisionCode))
{
metadata.Locus.DivisionCode = divisionCode;
}
else
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS_DIVISIONCODE);
throw new FormatException(message);
}
break;
case LOCUS_DATE:
DateTime date;
if (!string.IsNullOrWhiteSpace(value) && DateTime.TryParse(value, out date))
{
metadata.Locus.Date = date;
}
else
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS_DATE);
throw new FormatException(message);
}
break;
default:
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
LOCUS);
throw new FormatException(message);
}
rowIndex++;
}
return rowIndex;
}
/// <summary>
/// Validate GenBank LTR features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankLTRFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<LongTerminalRepeat> LTRFeatureList =
genMetadata.Features.LongTerminalRepeats;
var locBuilder = new LocationBuilder();
// Create a copy of Long Terminal Repeat feature.
LongTerminalRepeat cloneLTR = LTRFeatureList[0].Clone();
// Validate Long Terminal Repeat qualifiers.
Assert.AreEqual(LTRFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneLTR.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneLTR.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(LTRFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(LTRFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(LTRFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(LTRFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(LTRFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(LTRFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(LTRFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.LongTerminalRepeats[0].Location),
expectedLocation);
Assert.AreEqual(LTRFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(LTRFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(LTRFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(LTRFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(LTRFeatureList[0].StandardName));
// Create a new LTR and validate.
var ltr =
new LongTerminalRepeat(expectedLocation);
var ltrWithILoc = new LongTerminalRepeat(
genMetadata.Features.LongTerminalRepeats[0].Location);
// Set qualifiers and validate them.
ltr.Allele = expectedAllele;
ltr.GeneSymbol = geneSymbol;
ltrWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(ltr.GeneSymbol, geneSymbol);
Assert.AreEqual(ltr.Allele, expectedAllele);
Assert.AreEqual(ltrWithILoc.GenomicMapPosition,
expectedMap);
}
private void WriteReferences(GenBankMetadata metadata, TextWriter txtWriter)
{
if (metadata.References != null)
{
foreach (CitationReference reference in metadata.References)
{
// format the data for the first line
string data = reference.Number.ToString(CultureInfo.InvariantCulture);
if (!string.IsNullOrEmpty(reference.Location))
{
data = data.PadRight(3) + "(" + reference.Location + ")";
}
WriteHeaderSection("REFERENCE", data, txtWriter);
WriteHeaderSection(" AUTHORS", reference.Authors, txtWriter);
WriteHeaderSection(" CONSRTM", reference.Consortiums, txtWriter);
WriteHeaderSection(" TITLE", reference.Title, txtWriter);
WriteHeaderSection(" JOURNAL", reference.Journal, txtWriter);
WriteHeaderSection(" MEDLINE", reference.Medline, txtWriter);
WriteHeaderSection(" PUBMED", reference.PubMed, txtWriter);
WriteHeaderSection(" REMARK", reference.Remarks, txtWriter);
}
}
}
/// <summary>
/// Validate StemLoop features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankStemLoopFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<StemLoop> sLoopFeatureList = genMetadata.Features.StemLoops;
var locBuilder = new LocationBuilder();
// Create a copy of StemLoop feature.
StemLoop cloneSLoop = sLoopFeatureList[0].Clone();
// Validate transit peptide qualifiers.
Assert.AreEqual(sLoopFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneSLoop.GeneSymbol, geneSymbol);
Assert.AreEqual(cloneSLoop.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(sLoopFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(sLoopFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(sLoopFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(sLoopFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(sLoopFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(sLoopFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(sLoopFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.StemLoops[0].Location),
expectedLocation);
Assert.AreEqual(sLoopFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(sLoopFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(sLoopFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(sLoopFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(sLoopFeatureList[0].Operon));
Assert.IsTrue(string.IsNullOrEmpty(sLoopFeatureList[0].StandardName));
// Create a new StemLoop and validate the same.
var stemLoop = new StemLoop(expectedLocation);
var stemLoopWithILoc = new StemLoop(
genMetadata.Features.StemLoops[0].Location);
// Set qualifiers and validate them.
stemLoop.Allele = expectedAllele;
stemLoop.GeneSymbol = geneSymbol;
stemLoopWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(stemLoop.GeneSymbol, geneSymbol);
Assert.AreEqual(stemLoop.Allele, expectedAllele);
Assert.AreEqual(stemLoopWithILoc.GenomicMapPosition,
expectedMap);
}
private static void WriteLocus(ISequence sequence, TextWriter txtWriter)
{
// determine molecule and sequence type
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
GenBankLocusInfo locusInfo = null;
string molType = sequence.Alphabet.Name;
if (metadata != null)
{
locusInfo = metadata.Locus;
molType = locusInfo.MoleculeType.ToString();
}
string seqType;
if (sequence.Alphabet.Name != null)
{
if (molType == Alphabets.Protein.Name)
{
seqType = "aa";
molType = string.Empty; // protein files don't use molecule type
}
else
{
seqType = "bp";
}
}
else
{
if (sequence.Alphabet == Alphabets.Protein)
{
seqType = "aa";
molType = string.Empty; // protein files don't use molecule type
}
else
{
seqType = "bp";
if (sequence.Alphabet == Alphabets.DNA)
{
molType = Alphabets.DNA.Name;
}
else
{
molType = Alphabets.RNA.Name;
}
}
}
// retrieve metadata fields
string strandType = string.Empty;
string strandTopology = string.Empty;
string division = string.Empty;
DateTime date = DateTime.Now;
if (locusInfo != null)
{
strandType = Helper.GetStrandType(locusInfo.Strand);
strandTopology = Helper.GetStrandTopology(locusInfo.StrandTopology);
if (locusInfo.DivisionCode != SequenceDivisionCode.None)
{
division = locusInfo.DivisionCode.ToString();
}
date = locusInfo.Date;
}
txtWriter.WriteLine("{0,-12}{1,-16} {2,11} {3} {4,3}{5,-6} {6,-8} {7,3} {8}",
"LOCUS",
sequence.ID,
sequence.Count,
seqType,
strandType,
molType,
strandTopology,
division,
date.ToString("dd-MMM-yyyy", CultureInfo.InvariantCulture).ToUpperInvariant());
}
/// <summary>
/// Gives out string array of metadata and features just below metadata.
/// </summary>
/// <param name="metadata">GenBank Metadata</param>
/// <returns>string array of metadata</returns>
public static string[,] GenBankMetadataToRange(GenBankMetadata metadata)
{
List<string[]> excelData = new List<string[]>();
List<string> excelRow = new List<string>();
// Add the metadata headers
excelRow.Add(Properties.Resources.GenbankMetadataHeader);
excelData.Add(excelRow.ToArray());
excelRow.Clear();
if (metadata.Locus != null)
{
excelData.Add(new[] { Properties.Resources.GenbankMetadataLocus });
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataName, metadata.Locus.Name);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataSeqLength, metadata.Locus.SequenceLength.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataSeqType, metadata.Locus.SequenceType);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataStrandType, Helper.GetStrandType(metadata.Locus.Strand));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataMoleculeType, metadata.Locus.MoleculeType.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataStrandTopology, Helper.GetStrandTopology(metadata.Locus.StrandTopology));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataDivisionCode, metadata.Locus.DivisionCode.ToString());
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataDate, metadata.Locus.Date.ToString("dd-MMM-yyyy").ToUpper());
}
if (!string.IsNullOrWhiteSpace(metadata.Definition))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDefinition, "", metadata.Definition);
}
if (metadata.Accession != null)
{
string secondaryAccession = string.Empty;
foreach (string accession2 in metadata.Accession.Secondary)
{
secondaryAccession += accession2 == null ? " " : " " + accession2;
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataAccession, "", metadata.Accession.Primary + secondaryAccession);
}
if (metadata.DbLinks != null)
{
foreach (var link in metadata.DbLinks)
{
string linkNumbers = string.Empty;
foreach (string linkNumber in link.Numbers)
{
linkNumbers += linkNumber + ",";
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDBLink, "", link.Type.ToString() + ":" + linkNumbers);
}
}
if (!string.IsNullOrWhiteSpace(metadata.DbSource))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataDBSource, "", metadata.DbSource);
}
if (metadata.Version != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataVersion, "", (metadata.Version.Accession ?? string.Empty) + "." +
(metadata.Version.Version ?? string.Empty) + " " + Properties.Resources.GenbankMetadataGI + (metadata.Version.GiNumber ?? string.Empty));
}
if (metadata.Segment != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataSegment, "", metadata.Segment.Current + " of " + metadata.Segment.Count);
}
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataKeywords, "", metadata.Keywords);
if (metadata.Source != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataSource, "", metadata.Source.CommonName ?? string.Empty);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataOrganism, (metadata.Source.Organism.Genus ?? string.Empty) + " " + (metadata.Source.Organism.Species ?? string.Empty));
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataClassLevels, metadata.Source.Organism.ClassLevels ?? string.Empty);
}
foreach (CitationReference reference in metadata.References)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataReference, "", reference.Number.ToString() + " (" + reference.Location + ")");
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataAuthors, reference.Authors);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataTitle, reference.Title);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataJournal, reference.Journal);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataConsortiums, reference.Consortiums);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataMedLine, reference.Medline);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataPubMed, reference.PubMed);
AddNameValuePair(excelData, 1, Properties.Resources.GenbankMetadataRemarks, reference.Remarks);
}
if (!string.IsNullOrWhiteSpace(metadata.Primary))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataPrimary, "", metadata.Primary);
}
if (metadata.Comments != null && metadata.Comments.Count > 0)
{
StringBuilder strbuilder = null;
foreach (string str in metadata.Comments)
{
if (strbuilder == null)
{
strbuilder = new StringBuilder();
}
else
{
strbuilder.Append(Environment.NewLine);
}
strbuilder.Append(str);
}
if (strbuilder != null)
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataComment, "", strbuilder.ToString());
}
}
if (metadata.Features != null)
{
// Add the metadata headers
excelRow.Add(Properties.Resources.GenbankFeaturesHeader);
excelData.Add(excelRow.ToArray());
excelRow.Clear();
IList<FeatureItem> featureList = metadata.Features.All;
foreach (FeatureItem featureItem in featureList)
{
LocationBuilder locBuilder = new LocationBuilder();
// Add the feature headers
excelRow.Add(featureItem.Key);
//excelRow.Add(""); // skip one column
excelRow.Add(locBuilder.GetLocationString(featureItem.Location));
excelData.Add(excelRow.ToArray());
excelRow.Clear();
foreach (string key in featureItem.Qualifiers.Keys)
{
foreach (string value in featureItem.Qualifiers[key])
{
AddNameValuePair(excelData, 1, key, value);
}
}
}
}
if (!string.IsNullOrWhiteSpace(metadata.BaseCount))
{
AddNameValuePair(excelData, 0, Properties.Resources.GenbankMetadataBaseCount, "", metadata.BaseCount);
}
return ConvertToArray(excelData);
}
/// <summary>
/// Validate GenBank CDS features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankCDSFeatures(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
string expectedTranslation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankTranslationNode);
string expectedCodonStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CodonStartNode);
List<CodingSequence> codingSequenceFeatureList =
genMetadata.Features.CodingSequences;
var locBuilder = new LocationBuilder();
// Create a copy of Coding Seq Region feature.
CodingSequence cloneCDS = codingSequenceFeatureList[0].Clone();
// Validate Unsure Seq Region qualifiers.
Assert.AreEqual(codingSequenceFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneCDS.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneCDS.GeneSymbol, geneSymbol);
Assert.AreEqual(codingSequenceFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(codingSequenceFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(codingSequenceFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(codingSequenceFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.CodingSequences[0].Location),
expectedLocation);
Assert.AreEqual(codingSequenceFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(codingSequenceFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(codingSequenceFeatureList[0].CodonStart[0],
expectedCodonStart);
Assert.AreEqual(codingSequenceFeatureList[0].Translation,
expectedTranslation);
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].Codon.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].EnzymeCommissionNumber));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Number));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Operon));
Assert.IsFalse(codingSequenceFeatureList[0].Pseudo);
Assert.IsFalse(codingSequenceFeatureList[0].RibosomalSlippage);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].StandardName));
Assert.IsFalse(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationalExcept.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].TranslationTable));
Assert.IsFalse(codingSequenceFeatureList[0].TransSplicing);
Assert.IsTrue(string.IsNullOrEmpty(codingSequenceFeatureList[0].Exception));
// Create a new CDS feature using constructor.
var cds = new CodingSequence(expectedLocation);
var cdsWithLoc = new CodingSequence(
genMetadata.Features.CodingSequences[0].Location);
Sequence seq = cds.GetTranslation();
Assert.IsNotNull(seq);
// Set and validate qualifiers.
cds.Allele = expectedAllele;
cdsWithLoc.GeneSymbol = geneSymbol;
cdsWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(cdsWithLoc.GenomicMapPosition, expectedMap);
Assert.AreEqual(cds.Allele, expectedAllele);
Assert.AreEqual(cdsWithLoc.GeneSymbol, geneSymbol);
}
/// <summary>
/// Validate GenBank Non Coding RNA features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankNonCodingRNA(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNonCodingRnaClass = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.NonCodingRnaClassNode);
List<NonCodingRna> nonCodingRNAFeatureList =
genMetadata.Features.NonCodingRNAs;
var locBuilder = new LocationBuilder();
// Create a copy of Non coding RNA feature.
NonCodingRna cloneNonCodingRNA =
nonCodingRNAFeatureList[0].Clone();
// Validate Non Coding RNA Region qualifiers.
Assert.AreEqual(nonCodingRNAFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(nonCodingRNAFeatureList[0].NonCodingRnaClass,
expectedNonCodingRnaClass);
Assert.AreEqual(cloneNonCodingRNA.Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.NonCodingRNAs[0].Location),
expectedLocation);
// Create a non Coding RNA and validate the same.
var nRNA =
new NonCodingRna(genMetadata.Features.NonCodingRNAs[0].Location);
var nRNAWithLocation =
new NonCodingRna(expectedLocation);
// Set properties
nRNA.NonCodingRnaClass = expectedNonCodingRnaClass;
nRNAWithLocation.NonCodingRnaClass = expectedNonCodingRnaClass;
// Validate created nRNA.
Assert.AreEqual(nRNA.NonCodingRnaClass,
expectedNonCodingRnaClass);
Assert.AreEqual(nRNAWithLocation.NonCodingRnaClass,
expectedNonCodingRnaClass);
}
/// <summary>
/// Validate GenBank RibosomeBindingSite features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankRibosomeBindingSite(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<RibosomeBindingSite> ribosomeSite =
genMetadata.Features.RibosomeBindingSites;
// Create a copy of RibosomeBindigSite Region feature.
RibosomeBindingSite cloneRibosomeSite =
ribosomeSite[0].Clone();
var locBuilder = new LocationBuilder();
// Validate RibosomeBindigSite qualifiers.
Assert.AreEqual(ribosomeSite.Count.ToString((IFormatProvider) null)
, featureCount);
Assert.AreEqual(cloneRibosomeSite.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneRibosomeSite.GeneSymbol,
geneSymbol);
Assert.AreEqual(ribosomeSite[0].Allele,
expectedAllele);
Assert.AreEqual(ribosomeSite[0].Citation[0],
expectedCitation);
Assert.AreEqual(ribosomeSite[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(ribosomeSite[0].Inference[0],
expectedInference);
Assert.AreEqual(ribosomeSite[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.RibosomeBindingSites[0].Location),
expectedLocation);
Assert.AreEqual(ribosomeSite[0].Note[0],
expectedNote);
Assert.AreEqual(ribosomeSite[0].GenomicMapPosition,
expectedMap);
Assert.IsNotNull(ribosomeSite[0].OldLocusTag[0]);
Assert.IsNotNull(ribosomeSite[0].LocusTag[0]);
Assert.IsNotNull(ribosomeSite[0].StandardName);
// Create a new RibosomeBindingSite feature using constructor.
var ribosomeBindingSite =
new RibosomeBindingSite(expectedLocation);
var ribosomeBindingSiteLoc =
new RibosomeBindingSite(
genMetadata.Features.RibosomeBindingSites[0].Location);
// Set and validate qualifiers.
ribosomeBindingSite.Allele = expectedAllele;
ribosomeBindingSiteLoc.GeneSymbol = geneSymbol;
ribosomeBindingSiteLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(ribosomeBindingSiteLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(ribosomeBindingSite.Allele, expectedAllele);
Assert.AreEqual(ribosomeBindingSiteLoc.GeneSymbol,
geneSymbol);
}
/// <summary>
/// Validate GenBank UnsureSequenceRegion features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankUnsureSequenceRegion(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<UnsureSequenceRegion> unsureSeqRegionFeatureList =
genMetadata.Features.UnsureSequenceRegions;
// Create a copy of Unsure Seq Region feature.
UnsureSequenceRegion cloneUnSureSeqRegion =
unsureSeqRegionFeatureList[0].Clone();
var locBuilder = new LocationBuilder();
// Validate Unsure Seq Region qualifiers.
Assert.AreEqual(unsureSeqRegionFeatureList.Count.ToString((IFormatProvider) null)
, featureCount);
Assert.AreEqual(cloneUnSureSeqRegion.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(cloneUnSureSeqRegion.GeneSymbol,
geneSymbol);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(unsureSeqRegionFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.UnsureSequenceRegions[0].Location),
expectedLocation);
Assert.AreEqual(unsureSeqRegionFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(unsureSeqRegionFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.IsFalse(string.IsNullOrEmpty(unsureSeqRegionFeatureList[0].Compare.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(unsureSeqRegionFeatureList[0].Replace));
// Create a new Unsure feature using constructor.
var unsureRegion =
new UnsureSequenceRegion(expectedLocation);
var unsureRegionWithLoc =
new UnsureSequenceRegion(
genMetadata.Features.UnsureSequenceRegions[0].Location);
// Set and validate qualifiers.
unsureRegion.Allele = expectedAllele;
unsureRegionWithLoc.GeneSymbol = geneSymbol;
unsureRegionWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(unsureRegionWithLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(unsureRegion.Allele, expectedAllele);
Assert.AreEqual(unsureRegionWithLoc.GeneSymbol,
geneSymbol);
}
/// <summary>
/// Validate GenBank Operon features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankOperon(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<OperonRegion> operonFeatureList =
genMetadata.Features.OperonRegions;
var locBuilder = new LocationBuilder();
// Create a copy of Long Terminal Repeat feature.
OperonRegion cloneOperon = operonFeatureList[0].Clone();
// Validate Operon region qualifiers.
Assert.AreEqual(operonFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneOperon.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(operonFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(operonFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(operonFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(operonFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(operonFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(operonFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.OperonRegions[0].Location),
expectedLocation);
Assert.AreEqual(operonFeatureList[0].Note[0],
expectedNote);
Assert.IsFalse(string.IsNullOrEmpty(operonFeatureList[0].Function.ToString()));
Assert.AreEqual(operonFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.IsTrue(string.IsNullOrEmpty(operonFeatureList[0].Operon));
Assert.IsFalse(string.IsNullOrEmpty(operonFeatureList[0].Phenotype.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(operonFeatureList[0].StandardName));
Assert.IsFalse(operonFeatureList[0].Pseudo);
// Create a new Operon feature using constructor.
var operonRegion =
new OperonRegion(expectedLocation);
var operonRegionWithLoc = new OperonRegion(
genMetadata.Features.OperonRegions[0].Location);
// Set and validate qualifiers.
operonRegion.Allele = expectedAllele;
operonRegionWithLoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(operonRegionWithLoc.GenomicMapPosition,
expectedMap);
Assert.AreEqual(operonRegion.Allele, expectedAllele);
}
/// <summary>
/// Validate PrecursorRNA features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankPrecursorRNAFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedFunction = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FunctionNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<PrecursorRna> precursorRNAFeatureList =
genMetadata.Features.PrecursorRNAs;
var locBuilder = new LocationBuilder();
// Create a copy of Precursor RNA feature.
PrecursorRna clonePrecursorRNA =
precursorRNAFeatureList[0].Clone();
// Validate Precursor RNA qualifiers.
Assert.AreEqual(precursorRNAFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(clonePrecursorRNA.GeneSymbol,
geneSymbol);
Assert.AreEqual(clonePrecursorRNA.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(precursorRNAFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(precursorRNAFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(precursorRNAFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(precursorRNAFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(precursorRNAFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(precursorRNAFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(precursorRNAFeatureList[0].Label, expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.PrecursorRNAs[0].Location),
expectedLocation);
Assert.AreEqual(precursorRNAFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(precursorRNAFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(precursorRNAFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.AreEqual(precursorRNAFeatureList[0].Function[0],
expectedFunction);
Assert.IsTrue(string.IsNullOrEmpty(precursorRNAFeatureList[0].StandardName));
Assert.IsFalse(string.IsNullOrEmpty(precursorRNAFeatureList[0].Product.ToString()));
Assert.IsTrue(string.IsNullOrEmpty(precursorRNAFeatureList[0].Operon));
Assert.IsFalse(precursorRNAFeatureList[0].TransSplicing);
// Create a new Precursor RNA and validate the same.
var precursorRNA = new PrecursorRna(expectedLocation);
var precursorRNAWithILoc = new PrecursorRna(
genMetadata.Features.PrecursorRNAs[0].Location);
// Set qualifiers and validate them.
precursorRNA.Allele = expectedAllele;
precursorRNA.GeneSymbol = geneSymbol;
precursorRNAWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(precursorRNA.GeneSymbol, geneSymbol);
Assert.AreEqual(precursorRNA.Allele, expectedAllele);
Assert.AreEqual(precursorRNAWithILoc.GenomicMapPosition, expectedMap);
}
/// <summary>
/// Validate ModifiedBase features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankModifiedBaseFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<ModifiedBase> modifiedBaseFeatureList =
genMetadata.Features.ModifiedBases;
var locBuilder = new LocationBuilder();
// Create a copy of Modified base feature.
ModifiedBase cloneModifiedBase = modifiedBaseFeatureList[0].Clone();
// Validate Modified Base qualifiers.
Assert.AreEqual(modifiedBaseFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneModifiedBase.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneModifiedBase.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(modifiedBaseFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(modifiedBaseFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(modifiedBaseFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(modifiedBaseFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(modifiedBaseFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(modifiedBaseFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(modifiedBaseFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.ModifiedBases[0].Location),
expectedLocation);
Assert.AreEqual(modifiedBaseFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(modifiedBaseFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(modifiedBaseFeatureList[0].LocusTag[0],
expectedLocusTag);
Assert.IsFalse(string.IsNullOrEmpty(modifiedBaseFeatureList[0].ModifiedNucleotideBase.ToString()));
// Create a new ModifiedBase and validate the same.
var modifiedBase = new ModifiedBase(expectedLocation);
var modifiedBaseWithILoc = new ModifiedBase(
genMetadata.Features.ModifiedBases[0].Location);
// Set qualifiers and validate them.
modifiedBase.Allele = expectedAllele;
modifiedBase.GeneSymbol = geneSymbol;
modifiedBaseWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(modifiedBase.GeneSymbol, geneSymbol);
Assert.AreEqual(modifiedBase.Allele, expectedAllele);
Assert.AreEqual(modifiedBaseWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Parses the GenBank Origin data from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="metadata">The GenBank metadata.</param>
/// <param name="stream">The stream reader.</param>
private void ParseOrigin(ref string line, GenBankMetadata metadata, StreamReader stream)
{
// The origin line can contain optional data; don't put empty string into
// metadata.
string lineData = GetLineData(line, DataIndent);
if (!String.IsNullOrEmpty(lineData))
{
metadata.Origin = lineData;
}
line = GoToNextLine(line, stream);
IAlphabet alphabet = null;
var sequenceBuilder = new StringBuilder();
while ((line != null) && line[0] == ' ')
{
// Using a regex is too slow.
int len = line.Length;
int k = 0;
while (k < len && (line[k] == ' ' || Char.IsNumber(line[k])))
k++;
while (k < len)
{
string seqData = line.Substring(k, Math.Min(10, len - k));
sequenceBuilder.Append(seqData);
k += 11;
}
line = GoToNextLine(line, stream);
}
var sequenceString = sequenceBuilder.ToString().Trim();
if (!string.IsNullOrEmpty(sequenceString))
{
if (Alphabet == null)
{
byte[] tempData = UTF8Encoding.UTF8.GetBytes(sequenceString.ToUpperInvariant());
alphabet = Alphabets.AutoDetectAlphabet(tempData, 0, tempData.Length, alphabet);
if (alphabet == null)
{
var message = String.Format(CultureInfo.InvariantCulture, Properties.Resource.InvalidSymbolInString, line);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
alphabet = Alphabet;
}
sequenceWithData = new Sequence(alphabet, sequenceString);
}
}
/// <summary>
/// Parses the GenBank headers from the GenBank file.
/// parses everything before the features section
/// </summary>
/// <param name="sequence">The sequence.</param>
/// <param name="noOfSequence">The current sequence index.</param>
/// <param name="line">parse line</param>
/// <param name="stream">The stream reader.</param>
/// <returns>The parsed line.</returns>
private string ParseHeaders(ref Sequence sequence, int noOfSequence, string line, StreamReader stream)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
string data;
string[] tokens;
// only allow one locus line
bool haveParsedLocus = false;
string lineData;
if (noOfSequence == 0)
{
line = string.Empty;
line = GoToNextLine(line, stream);
}
// parse until we hit the features or sequence section
bool haveFinishedHeaders = false;
while ((line != null) && !haveFinishedHeaders)
{
switch (GetLineHeader(line, DataIndent))
{
case "LOCUS":
if (haveParsedLocus)
{
string message = String.Format(CultureInfo.CurrentCulture, Properties.Resource.ParserSecondLocus);
Trace.Report(message);
throw new InvalidDataException(message);
}
line = ParseLocusByTokens(line, ref sequence, stream);
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
haveParsedLocus = true;
// don't go to next line; current line still needs to be processed
break;
case "VERSION":
lineData = GetLineData(line, DataIndent);
tokens = lineData.Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
// first token contains accession and version
Match m = Regex.Match(tokens[0], @"^(?<accession>\w+)\.(?<version>\d+)$");
metadata.Version = new GenBankVersion();
if (m.Success)
{
metadata.Version.Version = m.Groups["version"].Value;
// The first token in the data from the accession line is referred to as
// the primary accession number, and should be the one used here in the
// version line.
string versionLineAccession = m.Groups["accession"].Value;
if (metadata.Accession == null)
{
ApplicationLog.WriteLine("WARN: VERSION processed before ACCESSION");
}
else
{
if (!versionLineAccession.Equals(metadata.Accession.Primary))
{
ApplicationLog.WriteLine("WARN: VERSION tag doesn't match ACCESSION");
}
else
{
metadata.Version.Accession = metadata.Accession.Primary;
}
}
}
if (tokens.Length > 1)
{
// second token contains primary ID
m = Regex.Match(tokens[1], @"^GI:(?<primaryID>.*)");
if (m.Success)
{
metadata.Version.GiNumber = m.Groups["primaryID"].Value;
}
}
line = GoToNextLine(line, stream);
break;
case "PROJECT":
lineData = GetLineData(line, DataIndent);
tokens = lineData.Split(':');
if (tokens.Length == 2)
{
metadata.Project = new ProjectIdentifier {
Name = tokens[0]
};
tokens = tokens[1].Split(',');
for (int i = 0; i < tokens.Length; i++)
{
metadata.Project.Numbers.Add(tokens[i]);
}
}
else
{
ApplicationLog.WriteLine("WARN: unexpected PROJECT header: " + line);
}
line = GoToNextLine(line, stream);
break;
case "SOURCE":
line = ParseSource(line, ref sequence, stream);
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "REFERENCE":
line = ParseReferences(line, ref sequence, stream); // can encounter more than one
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "COMMENT":
line = ParseComments(line, ref sequence, stream); // can encounter more than one
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "PRIMARY":
// This header is followed by sequence info in a table format that could be
// stored in a custom object. The first line contains column headers.
// For now, just validate the presence of the headers, and save the data
// as a string.
lineData = GetLineData(line, DataIndent);
tokens = lineData.Split("\t ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
// Validating for minimum two headers.
if (tokens.Length != 4)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserPrimaryLineError,
line);
Trace.Report(message);
throw new InvalidDataException(message);
}
string primaryData = ParseMultiLineData(ref line, Environment.NewLine, DataIndent, stream);
metadata.Primary = primaryData;
// don't go to next line; current line still needs to be processed
break;
// all the following are extracted the same way - possibly multiline
case "DEFINITION":
metadata.Definition = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "ACCESSION":
data = ParseMultiLineData(ref line, " ", DataIndent, stream);
metadata.Accession = new GenBankAccession();
string[] accessions = data.Split(' ');
metadata.Accession.Primary = accessions[0];
for (int i = 1; i < accessions.Length; i++)
{
metadata.Accession.Secondary.Add(accessions[i]);
}
break;
case "DBLINK":
data = ParseMultiLineData(ref line, "\n", DataIndent, stream);
metadata.DbLinks = new List <CrossReferenceLink>();
foreach (string link in data.Split('\n'))
{
tokens = link.Split(':');
if (tokens.Length == 2)
{
CrossReferenceLink newLink = new CrossReferenceLink();
if (string.Compare(tokens[0], CrossReferenceType.Project.ToString(), StringComparison.OrdinalIgnoreCase) == 0)
{
newLink.Type = CrossReferenceType.Project;
}
else if (string.Compare(tokens[0], CrossReferenceType.BioProject.ToString(), StringComparison.OrdinalIgnoreCase) == 0)
{
newLink.Type = CrossReferenceType.BioProject;
}
else
{
newLink.Type = CrossReferenceType.None;
if (string.Compare(tokens[0], TraceAssemblyArchive, StringComparison.OrdinalIgnoreCase) == 0)
{
newLink.Type = CrossReferenceType.TraceAssemblyArchive;
}
}
tokens = tokens[1].Split(',');
for (int i = 0; i < tokens.Length; i++)
{
newLink.Numbers.Add(tokens[i]);
}
metadata.DbLinks.Add(newLink);
}
else
{
ApplicationLog.WriteLine("WARN: unexpected DBLINK header: " + line);
}
}
break;
case "DBSOURCE":
metadata.DbSource = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "KEYWORDS":
metadata.Keywords = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "SEGMENT":
data = ParseMultiLineData(ref line, " ", DataIndent, stream);
const string delimeter = "of";
tokens = data.Split(delimeter.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
if (tokens.Length == 2)
{
metadata.Segment = new SequenceSegment();
int outvalue;
if (int.TryParse(tokens[0].Trim(), out outvalue))
{
metadata.Segment.Current = outvalue;
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + line);
}
if (int.TryParse(tokens[1].Trim(), out outvalue))
{
metadata.Segment.Count = outvalue;
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + line);
}
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + line);
}
break;
// all the following indicate sections beyond the headers parsed by this method
case "FEATURES":
case "BASE COUNT":
case "ORIGIN":
case "CONTIG":
haveFinishedHeaders = true;
break;
default:
string lineHeader = GetLineHeader(line, DataIndent);
lineData = GetLineData(line, DataIndent);
ApplicationLog.WriteLine(ToString() + "WARN: unknown {0} -> {1}", lineHeader, lineData);
string errMessage = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParseHeaderError,
lineHeader);
Trace.Report(errMessage);
throw new InvalidDataException(errMessage);
}
}
// check for required features
if (!haveParsedLocus)
{
string message = string.Format(CultureInfo.CurrentCulture, Properties.Resource.INVALID_INPUT_FILE, Name);
Trace.Report(message);
throw new InvalidDataException(message);
}
return(line);
}
/// <summary>
/// Parses the GenBank source data from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="sequence">The sequence.</param>
/// <param name="stream">The stream reader.</param>
/// <returns>The parsed line.</returns>
private string ParseSource(string line, ref Sequence sequence, StreamReader stream)
{
string source = string.Empty;
string organism = string.Empty;
string classLevels = string.Empty;
while (line != null)
{
string lineHeader = GetLineHeader(line, DataIndent);
string lineData;
if (lineHeader == "SOURCE")
{
// data can be multiline. spec says last line must end with period
// (note: this doesn't apply unless multiline)
bool lastDotted = true;
lineData = GetLineData(line, DataIndent);
source = lineData;
line = GoToNextLine(line, stream);
lineHeader = GetLineHeader(line, DataIndent);
while ((line != null) && (lineHeader == string.Empty))
{
source += " " + GetLineData(line, DataIndent);
lastDotted = (source.EndsWith(".", StringComparison.Ordinal));
line = GoToNextLine(line, stream);
lineHeader = GetLineHeader(line, DataIndent);
}
if (!lastDotted && Trace.Want(Trace.SeqWarnings))
{
Trace.Report("GenBank.ParseSource", Properties.Resource.OutOfSpec, source);
}
// don't go to next line; current line still needs to be processed
}
else if (line[0] == ' ')
{
if (lineHeader != "ORGANISM")
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidSourceField,
lineHeader);
Trace.Report(message);
throw new InvalidDataException(message);
}
lineData = GetLineData(line, DataIndent);
// this also can be multiline
organism = lineData;
line = GoToNextLine(line, stream);
lineHeader = GetLineHeader(line, DataIndent);
while ((line != null) && (lineHeader == string.Empty))
{
if (line.EndsWith(";", StringComparison.Ordinal) || line.EndsWith(".", StringComparison.Ordinal))
{
if (!String.IsNullOrEmpty(classLevels))
{
classLevels += " ";
}
lineData = GetLineData(line, DataIndent);
classLevels += lineData;
}
else
{
organism += " " + lineData;
}
line = GoToNextLine(line, stream);
lineHeader = GetLineHeader(line, DataIndent);
}
// don't go to next line; current line still needs to be processed
}
else
{
// don't go to next line; current line still needs to be processed
break;
}
}
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
metadata.Source = new SequenceSource {
CommonName = source
};
if (!string.IsNullOrEmpty(organism))
{
int index = organism.IndexOf(" ", StringComparison.Ordinal);
if (index > 0)
{
metadata.Source.Organism.Genus = organism.Substring(0, index);
if (organism.Length > index)
{
index++;
metadata.Source.Organism.Species = organism.Substring(index, organism.Length - index);
}
}
else
{
metadata.Source.Organism.Genus = organism;
}
}
metadata.Source.Organism.ClassLevels = classLevels;
if (classLevels.TrimEnd('.').Length > 0)
{
string genus = classLevels.TrimEnd('.').Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries).Last().Trim();
if (!genus.Equals(metadata.Source.Organism.Genus.Trim()))
{
metadata.Source.Organism.Species = organism;
metadata.Source.Organism.Genus = genus;
}
}
return(line);
}
private void WriteSource(GenBankMetadata metadata, TextWriter txtWriter)
{
if (metadata.Source != null)
{
string commonname = string.Empty;
if (!string.IsNullOrEmpty(metadata.Source.CommonName))
{
commonname = metadata.Source.CommonName;
}
WriteHeaderSection("SOURCE", commonname, txtWriter);
string organism = string.Empty;
if (!commonname.Equals(metadata.Source.Organism.Species))
{
if (!string.IsNullOrEmpty(metadata.Source.Organism.Genus))
{
organism += metadata.Source.Organism.Genus;
}
organism += " ";
}
if (!string.IsNullOrEmpty(metadata.Source.Organism.Species))
{
organism += metadata.Source.Organism.Species;
}
// Organism might be empty, trim the value to ensure that a string with one space is not written (writer fails on this)
WriteHeaderSection(" ORGANISM", organism.Trim(), txtWriter);
WriteHeaderSection(string.Empty, metadata.Source.Organism.ClassLevels, txtWriter);
}
}
/// <summary>
/// Helper method to parse the feature of gen bank data
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseGenBankFeatures(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string message = string.Empty;
string key;
string subKey;
string value = string.Empty;
while (rowIndex < cellRange.GetLength(0))
{
if (null != cellRange[rowIndex, KeyColumnIndex])
{
key = cellRange[rowIndex, KeyColumnIndex].ToString().ToUpperInvariant();
if (key.Equals(METADATA))
{
break;
}
}
else
{
rowIndex++;
continue;
}
if (3 > cellRange.GetLength(1))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
REFERENCE);
throw new FormatException(message);
}
subKey = cellRange[rowIndex, SubKeyColumnIndex] != null ? cellRange[rowIndex, SubKeyColumnIndex].ToString() : string.Empty;
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
if (key.Equals(BASECOUNT))
{
metadata.BaseCount = value;
rowIndex++;
}
else if (!string.IsNullOrWhiteSpace(value) && !string.IsNullOrWhiteSpace(key))
{
FeatureItem featureItem = StandardFeatureMap.GetStandardFeatureItem(new FeatureItem(key, value));
if (metadata.Features == null)
{
metadata.Features = new SequenceFeatures();
}
metadata.Features.All.Add(featureItem);
rowIndex++;
rowIndex = ParseQualifiers(featureItem, cellRange, rowIndex);
}
else
{
rowIndex++;
}
}
return rowIndex;
}
// Writes the comments, which are stored in a list of strings.
private void WriteComments(GenBankMetadata metadata, TextWriter txtWriter)
{
foreach (string comment in metadata.Comments)
{
WriteHeaderSection("COMMENT", comment, txtWriter);
}
}
/// <summary>
/// Validate GenBank GCSignal features
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="genMetadata">GenBank Metadata</param>
private void ValidateGenBankGCSignalFeature(string nodeName,
GenBankMetadata genMetadata)
{
// Get Values from XML node.
string expectedLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Location);
string expectedAllele = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlleleNode);
string featureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QualifierCount);
string expectedDbReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DbReferenceNode);
string geneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
string expectedCitation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CitationNode);
string expectedExperiment = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExperimentNode);
string expectedGeneSynonym = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSynonymNode);
string expectedInference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InferenceNode);
string expectedLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LabelNode);
string expectedLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LocusTagNode);
string expectedNote = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Note);
string expectedOldLocusTag = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OldLocusTagNode);
string expectedMap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenbankMapNode);
List<GcSingal> gcSignalFeatureList = genMetadata.Features.GCSignals;
var locBuilder = new LocationBuilder();
// Create a copy of GC_Signal feature.
GcSingal cloneGCSignal = gcSignalFeatureList[0].Clone();
// Validate GC_Signal qualifiers.
Assert.AreEqual(gcSignalFeatureList.Count.ToString((IFormatProvider) null),
featureCount);
Assert.AreEqual(cloneGCSignal.GeneSymbol,
geneSymbol);
Assert.AreEqual(cloneGCSignal.DatabaseCrossReference[0],
expectedDbReference);
Assert.AreEqual(gcSignalFeatureList[0].Allele,
expectedAllele);
Assert.AreEqual(gcSignalFeatureList[0].Citation[0],
expectedCitation);
Assert.AreEqual(gcSignalFeatureList[0].Experiment[0],
expectedExperiment);
Assert.AreEqual(gcSignalFeatureList[0].GenomicMapPosition,
expectedMap);
Assert.AreEqual(gcSignalFeatureList[0].GeneSynonym[0],
expectedGeneSynonym);
Assert.AreEqual(gcSignalFeatureList[0].Inference[0],
expectedInference);
Assert.AreEqual(gcSignalFeatureList[0].Label,
expectedLabel);
Assert.AreEqual(locBuilder.GetLocationString(
genMetadata.Features.GCSignals[0].Location),
expectedLocation);
Assert.AreEqual(gcSignalFeatureList[0].Note[0],
expectedNote);
Assert.AreEqual(gcSignalFeatureList[0].OldLocusTag[0],
expectedOldLocusTag);
Assert.AreEqual(gcSignalFeatureList[0].LocusTag[0],
expectedLocusTag);
// Create a new GCSignal and validate the same.
var gcSignal = new GcSingal(expectedLocation);
var gcSignalWithILoc = new GcSingal(
genMetadata.Features.GCSignals[0].Location);
// Set qualifiers and validate them.
gcSignal.Allele = expectedAllele;
gcSignal.GeneSymbol = geneSymbol;
gcSignalWithILoc.GenomicMapPosition = expectedMap;
Assert.AreEqual(gcSignal.GeneSymbol, geneSymbol);
Assert.AreEqual(gcSignal.Allele, expectedAllele);
Assert.AreEqual(gcSignalWithILoc.GenomicMapPosition,
expectedMap);
}
/// <summary>
/// Parses the GenBank Origin data from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="metadata">The GenBank metadata.</param>
/// <param name="stream">The stream reader.</param>
private void ParseOrigin(ref string line, GenBankMetadata metadata, StreamReader stream)
{
// The origin line can contain optional data; don't put empty string into
// metadata.
string lineData = GetLineData(line, DataIndent);
if (!String.IsNullOrEmpty(lineData))
{
metadata.Origin = lineData;
}
line = GoToNextLine(line, stream);
IAlphabet alphabet = null;
var sequenceBuilder = new StringBuilder();
while ((line != null) && line[0] == ' ')
{
// Using a regex is too slow.
int len = line.Length;
int k = 0;
while (k < len && (line[k] == ' ' || Char.IsNumber(line[k])))
{
k++;
}
while (k < len)
{
string seqData = line.Substring(k, Math.Min(10, len - k));
sequenceBuilder.Append(seqData);
k += 11;
}
line = GoToNextLine(line, stream);
}
var sequenceString = sequenceBuilder.ToString().Trim();
if (!string.IsNullOrEmpty(sequenceString))
{
if (Alphabet == null)
{
byte[] tempData = UTF8Encoding.UTF8.GetBytes(sequenceString.ToUpperInvariant());
alphabet = Alphabets.AutoDetectAlphabet(tempData, 0, tempData.Length, alphabet);
if (alphabet == null)
{
var message = String.Format(CultureInfo.InvariantCulture, Properties.Resource.InvalidSymbolInString, line);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
alphabet = Alphabet;
}
sequenceWithData = new Sequence(alphabet, sequenceString);
}
}
/// <summary>
/// Construct initialization.
/// </summary>
/// <param name="fragList">Fragment list.</param>
/// <param name="maxOverlapLen">Minimum overlap length.</param>
private void Init(ObservableCollection<Fragment> fragList, DesignerSettings settings)
{
this.Overlaps = new List<Overlap>();
this.Settings = settings;
Thermodynamics.thal_results results = new Thermodynamics.thal_results();
Thermodynamics.p3_get_thermodynamic_values(Settings.TmThalParamPath, ref results);
String message = new String(results.msg);
message = message.Trim('\0');
if (!String.IsNullOrEmpty(message))
{
throw new TmThalParamException(message);
}
//forward
String seq_5 = "";
String seq_3 = "";
String name = "";
List<MiscFeature> featList = new List<MiscFeature>();
int pairIndex;
int len_5;
int len_3;
for (int i = 0; i < fragList.Count; i++)
{
name += fragList[i].Name;
seq_3 = fragList[i].GetString();
len_5 = Math.Min(settings.MaxLen_5, seq_5.Length);
len_3 = Math.Min(settings.MaxLen_3, seq_3.Length);
String overhang_5 = seq_5.Substring(seq_5.Length - len_5, len_5);
String geneSpecific_3 = seq_3.Substring(0, len_3);
String loc = (seq_5.Length + 1).ToString() + ".." + (seq_5.Length + seq_3.Length).ToString();
MiscFeature gene = new MiscFeature(loc);
gene.StandardName = fragList[i].Name;
featList.Add(gene);
seq_5 += seq_3;
if (i == 0)
{
pairIndex = fragList.Count;
Overlaps.Add(new Overlap(Designer.VectorLabel + fragList[i].Name + "-fwd", new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
else
{
pairIndex = 2 * fragList.Count - i;
Overlaps.Add(new Overlap(fragList[i].Name + "-fwd", new Sequence(Alphabets.AmbiguousDNA, overhang_5), new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
}
this.Sequence = new Sequence(Alphabets.AmbiguousDNA, seq_5);
//meta
GenBankMetadata meta = new GenBankMetadata();
meta.Locus = new GenBankLocusInfo();
meta.Locus.MoleculeType = MoleculeType.DNA;
meta.Locus.Name = name;
meta.Locus.Date = System.DateTime.Now;
meta.Locus.SequenceLength = seq_5.Length;
meta.Comments.Add("designed with mufasa");
meta.Definition = "synthetic construct";
meta.Features = new SequenceFeatures();
meta.Features.All.AddRange(featList);
this.Sequence.Metadata.Add("GenBank", meta);
//reverse
fragList.Add(new Fragment(fragList[0]));
fragList.RemoveAt(0);
seq_5 = "";
seq_3 = "";
for (int i = fragList.Count - 1; i >= 0; i--)
{
seq_5 = fragList[i].GetReverseComplementString();
len_5 = Math.Min(settings.MaxLen_5, seq_3.Length);
len_3 = Math.Min(settings.MaxLen_3, seq_5.Length);
String overhang_5 = seq_3.Substring(seq_3.Length - len_5, len_5);
String geneSpecific_3 = seq_5.Substring(0, len_3);
seq_3 += seq_5;
if (i == fragList.Count - 1)
{
pairIndex = 0;
Overlaps.Add(new Overlap(Designer.VectorLabel + fragList[i].Name + "-rev", new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
else
{
pairIndex = i + 1;
Overlaps.Add(new Overlap(fragList[i].Name + "-rev", new Sequence(Alphabets.AmbiguousDNA, overhang_5), new Sequence(Alphabets.AmbiguousDNA, geneSpecific_3), settings.TmThalSettings, pairIndex));
}
}
for (int i = 0; i < fragList.Count; i++)
{
//Duplex melting temperatures
Overlaps[i].HeterodimerMeltingTemperature = Overlaps[i].GetDuplexTemperature(Overlaps[Overlaps[i].PairIndex]);
}
}
/// <summary>
/// Parses the GenBank Reference information from the GenBank file.
/// </summary>
/// <param name="line">parse line</param>
/// <param name="sequence">The sequence.</param>
/// <param name="stream">The stream reader.</param>
/// <returns>The parsed line.</returns>
private string ParseReferences(string line, ref Sequence sequence, StreamReader stream)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
IList <CitationReference> referenceList = metadata.References;
CitationReference reference = null;
while (line != null)
{
string lineHeader = GetLineHeader(line, DataIndent);
if (lineHeader == "REFERENCE")
{
// add previous reference
if (reference != null)
{
referenceList.Add(reference);
}
// check for start/end e.g. (bases 1 to 118), or prose notes
string lineData = GetLineData(line, DataIndent);
Match m = Regex.Match(lineData, @"^(?<number>\d+)(\s+\((?<location>.*)\))?");
if (!m.Success)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserReferenceError,
lineData);
Trace.Report(message);
throw new InvalidDataException(message);
}
// create new reference
string number = m.Groups["number"].Value;
string location = m.Groups["location"].Value;
reference = new CitationReference();
int outValue;
if (!int.TryParse(number, out outValue))
{
throw new InvalidOperationException(string.Format(CultureInfo.CurrentCulture, Properties.Resource.InvalidRefNumber, number));
}
reference.Number = outValue;
reference.Location = location;
line = GoToNextLine(line, stream);
}
else if (line.StartsWith(" ", StringComparison.Ordinal))
{
switch (lineHeader)
{
// all the following are extracted the same way - possibly multiline
case "AUTHORS":
reference.Authors = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "CONSRTM":
reference.Consortiums = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "TITLE":
reference.Title = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "JOURNAL":
reference.Journal = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "REMARK":
reference.Remarks = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "MEDLINE":
reference.Medline = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
case "PUBMED":
reference.PubMed = ParseMultiLineData(ref line, " ", DataIndent, stream);
break;
default:
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidReferenceField,
lineHeader);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
else
{
// add last reference
if (reference != null)
{
referenceList.Add(reference);
}
// don't go to next line; current line still needs to be processed
break;
}
}
return(line);
}
/// <summary>
/// This method transfers all available features from the MBF sequence and
/// populate them into biopatml features data type.
/// In this version only its name, start and end location is populated.
/// </summary>
/// <param name="metadata"></param>
/// <returns></returns>
private FeatureList ExtractFeatures(GenBankMetadata metadata)
{
List<FeatureItem> mbfFeatures = metadata.Features.All;
FeatureList bioFeatureList = new FeatureList();
foreach (FeatureItem item in mbfFeatures)
{
#region Constructs the feature outline first
//Strand is always assumed to be forward +1
QUT.Bio.BioPatML.Sequences.Feature bioFeature = new QUT.Bio.BioPatML.Sequences.Feature
(item.Key, item.Location.Start, item.Location.End, 1);
bioFeatureList.Add(bioFeature);
#endregion
#region Adds the qualifier key and values to Feature using AnnotationList
AnnotationList annList = new AnnotationList();
foreach (KeyValuePair<string, List<string>> qualitfier in item.Qualifiers)
annList.Add(qualitfier.Key, qualitfier.Value[0]);
bioFeature.AddAnnotations(annList);
#endregion
}
return bioFeatureList;
}
// parses everything before the features section
private void ParseHeaders(BioTextReader bioReader, ref Sequence sequence)
{
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
string data = string.Empty;
string[] tokens = null;
// set data indent for headers
bioReader.DataIndent = _dataIndent;
// only allow one locus line
bool haveParsedLocus = false;
// parse until we hit the features or sequence section
bool haveFinishedHeaders = false;
while (bioReader.HasLines && !haveFinishedHeaders)
{
switch (bioReader.LineHeader)
{
case "LOCUS":
if (haveParsedLocus)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserSecondLocus,
bioReader.LocationString);
Trace.Report(message);
throw new InvalidDataException(message);
}
ParseLocus(bioReader, ref sequence);
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
haveParsedLocus = true;
// don't go to next line; current line still needs to be processed
break;
case "VERSION":
tokens = bioReader.LineData.Split(new char[] { ' ' },
StringSplitOptions.RemoveEmptyEntries);
// first token contains accession and version
Match m = Regex.Match(tokens[0], @"^(?<accession>\w+)\.(?<version>\d+)$");
metadata.Version = new GenBankVersion();
if (m.Success)
{
metadata.Version.Version = m.Groups["version"].Value;
// The first token in the data from the accession line is referred to as
// the primary accession number, and should be the one used here in the
// version line.
string versionLineAccession = m.Groups["accession"].Value;
if (metadata.Accession == null)
{
ApplicationLog.WriteLine("WARN: VERSION processed before ACCESSION");
}
else
{
if (!versionLineAccession.Equals(metadata.Accession.Primary))
{
ApplicationLog.WriteLine("WARN: VERSION tag doesn't match ACCESSION");
}
else
{
metadata.Version.Accession = metadata.Accession.Primary;
}
}
}
// second token contains primary ID
m = Regex.Match(tokens[1], @"^GI:(?<primaryID>.*)");
if (m.Success)
{
metadata.Version.GINumber = m.Groups["primaryID"].Value;
}
bioReader.GoToNextLine();
break;
case "PROJECT":
tokens = bioReader.LineData.Split(':');
if (tokens.Length == 2)
{
metadata.Project = new ProjectIdentifier();
metadata.Project.Name = tokens[0];
tokens = tokens[1].Split(',');
for (int i = 0; i < tokens.Length; i++)
{
metadata.Project.Numbers.Add(tokens[i]);
}
}
else
{
ApplicationLog.WriteLine("WARN: unexpected PROJECT header: " + bioReader.Line);
}
bioReader.GoToNextLine();
break;
case "SOURCE":
ParseSource(bioReader, ref sequence);
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "REFERENCE":
ParseReferences(bioReader, ref sequence); // can encounter more than one
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "COMMENT":
ParseComments(bioReader, ref sequence); // can encounter more than one
metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// don't go to next line; current line still needs to be processed
break;
case "PRIMARY":
// This header is followed by sequence info in a table format that could be
// stored in a custom object. The first line contains column headers.
// For now, just validate the presence of the headers, and save the data
// as a string.
int[] locs = new int[4];
locs[0] = bioReader.LineData.IndexOf("TPA_SPAN", StringComparison.Ordinal);
locs[1] = bioReader.LineData.IndexOf("PRIMARY_IDENTIFIER", StringComparison.Ordinal);
locs[2] = bioReader.LineData.IndexOf("PRIMARY_SPAN", StringComparison.Ordinal);
locs[3] = bioReader.LineData.IndexOf("COMP", StringComparison.Ordinal);
if (locs[0] < 0 || locs[1] < 0 || locs[2] < 0 || locs[3] < 0)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserPrimaryLineError,
bioReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
string primaryData = ParseMultiLineData(bioReader, Environment.NewLine);
metadata.Primary = primaryData;
// don't go to next line; current line still needs to be processed
break;
// all the following are extracted the same way - possibly multiline
case "DEFINITION":
metadata.Definition = ParseMultiLineData(bioReader, " ");
break;
case "ACCESSION":
data = ParseMultiLineData(bioReader, " ");
metadata.Accession = new GenBankAccession();
string[] accessions = data.Split(' ');
metadata.Accession.Primary = accessions[0];
for (int i = 1; i < accessions.Length; i++)
{
metadata.Accession.Secondary.Add(accessions[i]);
}
break;
case "DBLINK":
tokens = bioReader.LineData.Split(':');
if (tokens.Length == 2)
{
metadata.DBLink = new CrossReferenceLink();
if (string.Compare(tokens[0],
CrossReferenceType.Project.ToString(),
StringComparison.OrdinalIgnoreCase) == 0)
{
metadata.DBLink.Type = CrossReferenceType.Project;
}
else
{
metadata.DBLink.Type = CrossReferenceType.TraceAssemblyArchive;
}
tokens = tokens[1].Split(',');
for (int i = 0; i < tokens.Length; i++)
{
metadata.DBLink.Numbers.Add(tokens[i]);
}
}
else
{
ApplicationLog.WriteLine("WARN: unexpected DBLINK header: " + bioReader.Line);
}
bioReader.GoToNextLine();
break;
case "DBSOURCE":
metadata.DBSource = ParseMultiLineData(bioReader, " ");
break;
case "KEYWORDS":
metadata.Keywords = ParseMultiLineData(bioReader, " ");
break;
case "SEGMENT":
data = ParseMultiLineData(bioReader, " ");
string delimeter = "of";
tokens = data.Split(delimeter.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
int outvalue;
if (tokens.Length == 2)
{
metadata.Segment = new SequenceSegment();
if (int.TryParse(tokens[0].Trim(), out outvalue))
{
metadata.Segment.Current = outvalue;
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + bioReader.Line);
}
if (int.TryParse(tokens[1].Trim(), out outvalue))
{
metadata.Segment.Count = outvalue;
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + bioReader.Line);
}
}
else
{
ApplicationLog.WriteLine("WARN: unexpected SEGMENT header: " + bioReader.Line);
}
break;
// all the following indicate sections beyond the headers parsed by this method
case "FEATURES":
case "BASE COUNT":
case "ORIGIN":
case "CONTIG":
haveFinishedHeaders = true;
break;
default:
ApplicationLog.WriteLine(ToString() + "WARN: unknown {0} -> {1}", bioReader.LineHeader, bioReader.LineData);
string errMessage = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParseHeaderError,
bioReader.LineHeader);
Trace.Report(errMessage);
throw new InvalidDataException(errMessage);
}
}
// check for required features
if (!haveParsedLocus)
{
string message = string.Format(CultureInfo.CurrentCulture, Resource.INVAILD_INPUT_FILE, this.Name);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
// LOCUS is the first line in a GenBank record
private void ParseLocus(BioTextReader bioReader, ref Sequence sequence)
{
GenBankLocusInfo locusInfo = new GenBankLocusInfo();
// GenBank spec recommends token rather than position-based parsing, but this
// is only partially possible without making extra assumptions about the presence
// of optional fields.
string[] tokens = bioReader.LineData.Split(new char[] { ' ' },
StringSplitOptions.RemoveEmptyEntries);
sequence.ID = tokens[0];
locusInfo.Name = tokens[0];
int sequenceLength;
if (!int.TryParse(tokens[1], out sequenceLength))
{
throw new InvalidOperationException();
}
locusInfo.SequenceLength = sequenceLength;
string seqType = tokens[2];
if (seqType != "bp" && seqType != "aa")
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidLocus,
bioReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
// Determine format version and parse the remaining fields by position.
string strandType;
string strandTopology;
string division;
string rawDate;
string molType = string.Empty;
if (Helper.StringHasMatch(bioReader.GetLineField(31, 32), "bp", "aa"))
{
// older format
strandType = bioReader.GetLineField(34, 36).Trim();
strandTopology = bioReader.GetLineField(43, 52).Trim();
division = bioReader.GetLineField(53, 56).Trim();
rawDate = bioReader.GetLineField(63).Trim();
// molecule type field is not used for amino acid chains
if (seqType != "aa")
{
molType = bioReader.GetLineField(37, 42).Trim();
}
}
else
{
// newer format
strandType = bioReader.GetLineField(45, 47).Trim();
strandTopology = bioReader.GetLineField(56, 63).Trim();
division = bioReader.GetLineField(65, 67).Trim();
rawDate = bioReader.GetLineField(69).Trim();
// molecule type field is not used for amino acid chains
if (seqType != "aa")
{
molType = bioReader.GetLineField(48, 53).Trim();
}
}
// process strand type
if (!Helper.StringHasMatch(strandType, string.Empty, "ss-", "ds-", "ms-"))
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidLocus,
bioReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
locusInfo.Strand = Helper.GetStrandType(strandType);
// process strand topology
if (!Helper.StringHasMatch(strandTopology, string.Empty, "linear", "circular"))
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidStrand,
strandTopology);
Trace.Report(message);
throw new InvalidDataException(message);
}
locusInfo.StrandTopology = Helper.GetStrandTopology(strandTopology);
// process division
try
{
locusInfo.DivisionCode = (SequenceDivisionCode)Enum.Parse(typeof(SequenceDivisionCode), division);
}
catch (ArgumentException)
{
locusInfo.DivisionCode = SequenceDivisionCode.None;
}
// process date
DateTime date;
if (!DateTime.TryParse(rawDate, out date))
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidDate,
rawDate);
Trace.Report(message);
throw new FormatException(message);
}
locusInfo.Date = date;
locusInfo.SequenceType = seqType;
// process sequence type and molecule type
MoleculeType moleculeType;
if (seqType == "aa")
{
moleculeType = MoleculeType.Protein;
}
else
{
moleculeType = GetMoleculeType(molType);
if (moleculeType == MoleculeType.Invalid)
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidLocus,
bioReader.Line);
Trace.Report(message);
throw new FormatException(message);
}
}
IAlphabet alphabet = GetAlphabet(moleculeType);
if (alphabet != sequence.Alphabet)
{
if (Alphabet != null && Alphabet != alphabet)
{
string message = Properties.Resource.ParserIncorrectAlphabet;
Trace.Report(message);
throw new InvalidDataException(message);
}
sequence = new Sequence(alphabet, Encoding, sequence);
sequence.IsReadOnly = false;
}
sequence.MoleculeType = moleculeType;
locusInfo.MoleculeType = moleculeType;
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
metadata.Locus = locusInfo;
bioReader.GoToNextLine();
}
/// <summary>
/// Given range may contain normal metadata and features, if you can find
/// the heading 'Features' in any row of the range, anything below it is
/// part of features otherwise, try to parse everything as metadata.
/// </summary>
/// <param name="ranges">ranges</param>
/// <returns></returns>
public static GenBankMetadata RangeToGenBankMetadata(IList<Range> ranges)
{
GenBankMetadata metadata = new GenBankMetadata();
int height = 0, width = 0;
object[,] cellRange;
foreach (Range r in ranges)
{
height += r.Rows.Count;
width = width < r.Columns.Count ? r.Columns.Count : width;
}
cellRange = new object[height + 1, width + 1];
int k = 1;
foreach (Range r in ranges)
{
for (int i = 1; i <= r.Rows.Count; i++, k++)
{
for (int j = 1; j <= r.Columns.Count; j++)
{
cellRange[k, j] = r[i, j].Value2 as object;
}
}
}
int rowIndex = 1;
while (rowIndex < cellRange.GetLength(0))
{
if (null != cellRange[rowIndex, 1])
{
string cellValue = cellRange[rowIndex, 1].ToString().ToUpperInvariant();
switch (cellValue)
{
case METADATA:
rowIndex++;
rowIndex = ParseGenBankMetadata(metadata,
cellRange,
rowIndex);
break;
case FEATURES:
rowIndex++;
rowIndex = ParseGenBankFeatures(metadata,
cellRange,
rowIndex);
break;
default:
rowIndex++;
break;
}
}
else
{
rowIndex++;
}
}
return metadata;
}
private static void ParseSource(BioTextReader bioReader, ref Sequence sequence)
{
string source = string.Empty;
string organism = string.Empty;
string classLevels = string.Empty;
while (bioReader.HasLines)
{
if (bioReader.LineHeader == "SOURCE")
{
// data can be multiline. spec says last line must end with period
// (note: this doesn't apply unless multiline)
bool lastDotted = true;
source = bioReader.LineData;
bioReader.GoToNextLine();
while (bioReader.HasLines && !bioReader.LineHasHeader)
{
source += " " + bioReader.LineData;
lastDotted = (source.EndsWith(".", StringComparison.Ordinal));
bioReader.GoToNextLine();
}
if (!lastDotted && Trace.Want(Trace.SeqWarnings))
{
Trace.Report("GenBank.ParseSource", Properties.Resource.OutOfSpec, source);
}
// don't go to next line; current line still needs to be processed
}
else if (bioReader.Line[0] == ' ')
{
if (bioReader.LineHeader != "ORGANISM")
{
string message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserInvalidSourceField,
bioReader.LineHeader);
Trace.Report(message);
throw new InvalidDataException(message);
}
// this also can be multiline
organism = bioReader.LineData;
bioReader.GoToNextLine();
while (bioReader.HasLines && !bioReader.LineHasHeader)
{
if (bioReader.Line.EndsWith(";", StringComparison.Ordinal) || bioReader.Line.EndsWith(".", StringComparison.Ordinal))
{
if (!String.IsNullOrEmpty(classLevels))
{
classLevels += " ";
}
classLevels += bioReader.LineData;
}
else
{
organism += " " + bioReader.LineData;
}
bioReader.GoToNextLine();
}
// don't go to next line; current line still needs to be processed
}
else
{
// don't go to next line; current line still needs to be processed
break;
}
}
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
metadata.Source = new SequenceSource();
metadata.Source.CommonName = source;
if (!string.IsNullOrEmpty(organism))
{
int index = organism.IndexOf(" ", StringComparison.Ordinal);
if (index > 0)
{
metadata.Source.Organism.Genus = organism.Substring(0, index);
if (organism.Length > index)
{
index++;
metadata.Source.Organism.Species = organism.Substring(index, organism.Length - index);
}
}
else
{
metadata.Source.Organism.Genus = organism;
}
}
metadata.Source.Organism.ClassLevels = classLevels;
}
/// <summary>
/// Parses source info.
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseSource(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string Key;
string subKey;
string value;
string message;
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
rowIndex++;
while (rowIndex < cellRange.GetLength(0))
{
if (3 > cellRange.GetLength(1))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
SOURCE);
throw new FormatException(message);
}
if (null != cellRange[rowIndex, KeyColumnIndex])
{
Key = cellRange[rowIndex, KeyColumnIndex].ToString();
if (!string.IsNullOrWhiteSpace(Key))
{
break;
}
}
if (null == cellRange[rowIndex, SubKeyColumnIndex] || string.IsNullOrWhiteSpace(cellRange[rowIndex, SubKeyColumnIndex].ToString()))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
SOURCE);
throw new FormatException(message);
}
if (metadata.Source == null)
{
metadata.Source = new SequenceSource();
metadata.Source.CommonName = value;
}
subKey = cellRange[rowIndex, SubKeyColumnIndex].ToString().ToUpperInvariant();
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
if (metadata.Source.Organism == null)
{
metadata.Source.Organism = new OrganismInfo();
}
switch (subKey)
{
case SOURCE_ORGANISM:
if (string.IsNullOrWhiteSpace(value))
{
break;
}
string[] tokens = value.Split(" ".ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
metadata.Source.Organism.Genus = tokens[0];
if (tokens.Length > 1)
{
metadata.Source.Organism.Species = tokens[1];
for (int i = 2; i < tokens.Length; i++)
{
metadata.Source.Organism.Species = metadata.Source.Organism.Species + " " + tokens[i];
}
}
break;
case SOURCE_CLASSLEVELS:
metadata.Source.Organism.ClassLevels = value;
break;
}
rowIndex++;
}
return rowIndex;
}
// Handle optional BASE COUNT, then ORIGIN and sequence data.
private void ParseSequence(BioTextReader bioReader, ref Sequence sequence)
{
string message = string.Empty;
GenBankMetadata metadata = (GenBankMetadata)sequence.Metadata[Helper.GenBankMetadataKey];
// set data indent for sequence headers
bioReader.DataIndent = _dataIndent;
while (bioReader.HasLines)
{
if (bioReader.Line.StartsWith("//", StringComparison.Ordinal))
{
bioReader.GoToNextLine();
break; // end of sequence record
}
switch (bioReader.LineHeader)
{
case "BASE COUNT":
// The BASE COUNT linetype is obsolete and was removed
// from the GenBank flatfile format in October 2003. But if it is
// present, we will use it. We get the untrimmed version since it
// starts with a right justified column.
metadata.BaseCount = bioReader.Line.Substring(_dataIndent);
bioReader.GoToNextLine();
break;
case "ORIGIN":
// The origin line can contain optional data; don't put empty string into
// metadata.
if (!String.IsNullOrEmpty(bioReader.LineData))
{
metadata.Origin = bioReader.LineData;
}
bioReader.GoToNextLine();
IAlphabet alphabet = null;
while (bioReader.HasLines && bioReader.Line[0] == ' ')
{
// Using a regex is too slow.
int len = bioReader.Line.Length;
int k = 10;
while (k < len)
{
string seqData = bioReader.Line.Substring(k, Math.Min(10, len - k));
if (Alphabet == null)
{
alphabet = IdentifyAlphabet(alphabet, seqData);
if (alphabet == null)
{
message = String.Format(CultureInfo.CurrentCulture, Resource.InvalidSymbolInString, bioReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
if (sequence.Alphabet != alphabet)
{
Sequence seq = new Sequence(alphabet, Encoding, sequence);
seq.MoleculeType = sequence.MoleculeType;
seq.IsReadOnly = false;
sequence.Clear();
sequence = seq;
}
}
sequence.InsertRange(sequence.Count, seqData);
k += 11;
}
bioReader.GoToNextLine();
}
break;
case "CONTIG":
metadata.Contig = ParseMultiLineData(bioReader, Environment.NewLine);
// don't go to next line; current line still needs to be processed
break;
default:
message = String.Format(
CultureInfo.CurrentCulture,
Properties.Resource.ParserUnexpectedLineInSequence,
bioReader.Line);
Trace.Report(message);
throw new InvalidDataException(message);
}
}
}
/// <summary>
/// Helper method to parse the metadata of gen bank data
/// </summary>
/// <param name="metadata">Metadata object</param>
/// <param name="cellRange">Range of cells</param>
/// <param name="rowIndex">Current index of row</param>
/// <returns>Index of row</returns>
private static int ParseGenBankMetadata(GenBankMetadata metadata, object[,] cellRange, int rowIndex)
{
string message = string.Empty;
string key;
string subKey;
string value = string.Empty;
while (rowIndex < cellRange.GetLength(0))
{
if (null != cellRange[rowIndex, KeyColumnIndex] && !string.IsNullOrWhiteSpace(cellRange[rowIndex, KeyColumnIndex].ToString()))
{
key = cellRange[rowIndex, KeyColumnIndex].ToString().ToUpperInvariant();
if (key.Equals(FEATURES))
{
break;
}
}
else
{
rowIndex++;
continue;
}
subKey = cellRange[rowIndex, SubKeyColumnIndex] != null ? cellRange[rowIndex, SubKeyColumnIndex].ToString() : string.Empty;
value = cellRange[rowIndex, ValueColumnIndex] != null ? cellRange[rowIndex, ValueColumnIndex].ToString() : string.Empty;
string[] tokens;
switch (key)
{
case LOCUS:
rowIndex = ParseLocus(metadata, cellRange, rowIndex);
rowIndex--;
break;
case DEFINITION:
metadata.Definition = value;
break;
case ACCESSION:
metadata.Accession = new GenBankAccession();
if (string.IsNullOrWhiteSpace(value))
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
ACCESSION);
throw new FormatException(message);
}
string[] accessions = value.Split(' ');
metadata.Accession.Primary = accessions[0];
for (int i = 1; i < accessions.Length; i++)
{
metadata.Accession.Secondary.Add(accessions[i]);
}
break;
case DBLINK:
if (!string.IsNullOrWhiteSpace(value))
{
break;
}
tokens = value.Split(':');
if (tokens.Length == 2)
{
if (metadata.DbLinks == null)
{ metadata.DbLinks = new List<CrossReferenceLink>(2); }
var curLink = new CrossReferenceLink();
if (string.Compare(tokens[0],
CrossReferenceType.Project.ToString(),
StringComparison.OrdinalIgnoreCase) == 0)
{
curLink.Type = CrossReferenceType.Project;
}
else if (string.Compare(tokens[0],
CrossReferenceType.BioProject.ToString(),
StringComparison.OrdinalIgnoreCase) == 0)
{
curLink.Type = CrossReferenceType.BioProject;
}
else
{
curLink.Type = CrossReferenceType.TraceAssemblyArchive;
}
tokens = tokens[1].Split(',');
for (int i = 0; i < tokens.Length; i++)
{
curLink.Numbers.Add(tokens[i]);
}
metadata.DbLinks.Add(curLink);
}
break;
case DBSOURCE:
metadata.DbSource = value;
break;
case VERSION:
if (string.IsNullOrWhiteSpace(value))
{
break;
}
tokens = value.Split(new char[] { ' ' },
StringSplitOptions.RemoveEmptyEntries);
// first token contains accession and version
Match m = Regex.Match(tokens[0], @"^(?<accession>\w+)\.(?<version>\d+)$");
metadata.Version = new GenBankVersion();
if (m.Success)
{
metadata.Version.Version = m.Groups["version"].Value;
// The first token in the data from the accession line is referred to as
// the primary accession number, and should be the one used here in the
// version line.
metadata.Version.Accession = m.Groups["accession"].Value;
}
if (tokens.Length > 1)
{
// second token contains primary ID
m = Regex.Match(tokens[1], @"^GI:(?<primaryID>.*)");
if (m.Success)
{
metadata.Version.GiNumber = m.Groups["primaryID"].Value;
}
}
break;
case SEGMENT:
if (string.IsNullOrWhiteSpace(value))
{
break;
}
tokens = value.Split(" of ".ToArray(), StringSplitOptions.RemoveEmptyEntries);
if (tokens.Length == 2)
{
int current;
int count;
if (int.TryParse(tokens[0], out current))
{
if (int.TryParse(tokens[1], out count))
{
metadata.Segment = new SequenceSegment();
metadata.Segment.Current = current;
metadata.Segment.Count = count;
}
}
}
if (metadata.Segment == null)
{
message = String.Format(
CultureInfo.InvariantCulture,
Resources.UnrecognizedGenBankMetadataFormat,
ACCESSION);
throw new FormatException(message);
}
break;
case KEYWORDS:
metadata.Keywords = value;
break;
case SOURCE:
rowIndex = ParseSource(metadata, cellRange, rowIndex);
rowIndex--;
break;
case REFERENCE:
rowIndex = ParseReference(metadata, cellRange, rowIndex);
rowIndex--;
break;
case PRIMARY:
metadata.Primary = value;
break;
case COMMENT:
if (!string.IsNullOrWhiteSpace(value))
{
tokens = value.Split(Environment.NewLine.ToCharArray(), StringSplitOptions.RemoveEmptyEntries);
foreach (string str in tokens)
{
metadata.Comments.Add(str);
}
}
break;
}
rowIndex++;
}
return rowIndex;
}
/// <summary>
/// Validate GenBank features for medium size sequences.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">DNA,RNA or Protein method</param>
private void ValidateGenBankFeatures(string nodeName, string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string mRNAFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNACount);
string exonFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonCount);
string intronFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronCount);
string cdsFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCount);
string allFeaturesCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenBankFeaturesCount);
string expectedCDSKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSKey);
string expectedIntronKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronKey);
string expectedExonKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonKey);
string mRNAKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNAKey);
string sourceKeyName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SourceKey);
// Parse a file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> sequenceList = parserObj.Parse(filePath);
// GenBank metadata.
var metadata = new GenBankMetadata();
if (1 == sequenceList.Count())
{
metadata =
sequenceList.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
}
else
{
metadata =
sequenceList.ElementAt(1).Metadata[Constants.GenBank] as GenBankMetadata;
}
// Validate GenBank Features.
Assert.AreEqual(metadata.Features.All.Count,
Convert.ToInt32(allFeaturesCount, null));
Assert.AreEqual(metadata.Features.CodingSequences.Count,
Convert.ToInt32(cdsFeatureCount, null));
Assert.AreEqual(metadata.Features.Exons.Count,
Convert.ToInt32(exonFeatureCount, null));
Assert.AreEqual(metadata.Features.Introns.Count,
Convert.ToInt32(intronFeatureCount, null));
Assert.AreEqual(metadata.Features.MessengerRNAs.Count,
Convert.ToInt32(mRNAFeatureCount, null));
Assert.AreEqual(metadata.Features.Attenuators.Count, 0);
Assert.AreEqual(metadata.Features.CAATSignals.Count, 0);
Assert.AreEqual(metadata.Features.DisplacementLoops.Count, 0);
Assert.AreEqual(metadata.Features.Enhancers.Count, 0);
// Validate GenBank feature list.
if ((0 == string.Compare(methodName, "DNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
|| (0 == string.Compare(methodName, "RNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
IList<FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(featureList[0].Key.ToString(null), sourceKeyName);
Assert.AreEqual(featureList[1].Key.ToString(null), expectedCDSKey);
Assert.AreEqual(featureList[2].Key.ToString(null), expectedCDSKey);
Assert.AreEqual(featureList[10].Key.ToString(null), mRNAKey);
Assert.AreEqual(featureList[12].Key.ToString(null), expectedExonKey);
Assert.AreEqual(featureList[18].Key.ToString(null), expectedIntronKey);
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
else if ((0 == string.Compare(methodName, "Protein", CultureInfo.CurrentCulture,
CompareOptions.IgnoreCase)))
{
IList<FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(featureList[10].Key.ToString(null), expectedIntronKey);
Assert.AreEqual(featureList[18].Key.ToString(null), expectedExonKey);
ApplicationLog.WriteLine(
"GenBank Features P1: Successfully validated the GenBank Features");
}
}
}
