public void GenBankFeatures()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_singleProteinSeqGenBankFilename);
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
List <CodingSequence> CDS = metadata.Features.CodingSequences;
Assert.AreEqual(CDS.Count, 3);
Assert.AreEqual(CDS[0].DatabaseCrossReference.Count, 1);
Assert.AreEqual(CDS[0].GeneSymbol, string.Empty);
Assert.AreEqual(metadata.Features.GetFeatures("source").Count, 1);
Assert.IsFalse(CDS[0].Pseudo);
Assert.AreEqual(metadata.GetFeatures(1, 109).Count, 2);
Assert.AreEqual(metadata.GetFeatures(1, 10).Count, 2);
Assert.AreEqual(metadata.GetFeatures(10, 100).Count, 2);
Assert.AreEqual(metadata.GetFeatures(120, 150).Count, 2);
Assert.AreEqual(metadata.GetCitationsReferredInFeatures().Count, 0);
seq = parser.ParseOne(_genBankDataPath + @"\NC_001284.gbk");
metadata = seq.Metadata["GenBank"] as GenBankMetadata;
Assert.AreEqual(metadata.Features.All.Count, 743);
Assert.AreEqual(metadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(metadata.Features.Exons.Count, 32);
Assert.AreEqual(metadata.Features.Introns.Count, 22);
Assert.AreEqual(metadata.Features.Genes.Count, 60);
Assert.AreEqual(metadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(metadata.Features.Promoters.Count, 17);
Assert.AreEqual(metadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(metadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(metadata.Features.GetFeatures(StandardFeatureKeys.CodingSequence).Count, 117);
Assert.AreEqual(metadata.Features.CodingSequences[0].Translation.Trim('"'), metadata.Features.CodingSequences[0].GetTranslation().ToString());
Assert.AreEqual(2, metadata.GetFeatures(11918, 12241).Count);
}
public void GenBankFeatureClone()
{
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(@"testdata\GenBank\NC_001284.gbk");
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
Assert.AreEqual(metadata.Features.All.Count, 743);
Assert.AreEqual(metadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(metadata.Features.Exons.Count, 32);
Assert.AreEqual(metadata.Features.Introns.Count, 22);
Assert.AreEqual(metadata.Features.Genes.Count, 60);
Assert.AreEqual(metadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(metadata.Features.Promoters.Count, 17);
Assert.AreEqual(metadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(metadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(metadata.Features.CodingSequences[0].Translation.Trim('"'), metadata.Features.CodingSequences[0].GetTranslation().ToString());
Assert.AreEqual(metadata.GetFeatures(11918, 12241).Count, 2);
GenBankMetadata clonedMetadata = metadata.Clone();
Assert.AreEqual(clonedMetadata.Features.All.Count, 743);
Assert.AreEqual(clonedMetadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(clonedMetadata.Features.Exons.Count, 32);
Assert.AreEqual(clonedMetadata.Features.Introns.Count, 22);
Assert.AreEqual(clonedMetadata.Features.Genes.Count, 60);
Assert.AreEqual(clonedMetadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(clonedMetadata.Features.Promoters.Count, 17);
Assert.AreEqual(clonedMetadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(clonedMetadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(clonedMetadata.Features.CodingSequences[0].Translation.Trim('"'), clonedMetadata.Features.CodingSequences[0].GetTranslation().ToString());
Assert.AreEqual(clonedMetadata.GetFeatures(11918, 12241).Count, 2);
}
public void TestGenBankFailureWhenParsingEmpty()
{
ISequenceParser parser = new GenBankParser();
bool failed = false;
// test ParseOne
try
{
ISequence seq = parser.ParseOne(new StringReader(string.Empty));
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for calling ParseOne on reader containing empty string.");
}
// test Parse
try
{
IList <ISequence> seqList = parser.Parse(new StringReader(string.Empty));
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for calling Parse on reader containing empty string.");
}
}
/// <summary>
/// Extracts sequence from genbank file.
/// </summary>
/// <param name="id">
/// Accession id of the sequence in ncbi (remote id).
/// </param>
/// <returns>
/// The <see cref="Stream"/>.
/// </returns>
public static ISequence DownloadGenBankSequence(string id)
{
ISequenceParser parser = new GenBankParser();
string url = GetEfetchParamsString("gbwithparts") + id;
Stream dataStream = GetResponseStream(url);
return(parser.ParseOne(dataStream));
}
public void TestGenBankWhenParsingOneOfMany()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_multipleSeqGenBankFilename);
Assert.IsNotNull(seq);
}
public void TestGenBankLocusTokenParser()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_genBankFile_LocusTokenParserTest);
Assert.IsNotNull(seq);
}
public void TestGenBankFeaturesWithBinaryFormatter()
{
Stream stream = null;
try
{
stream = File.Open("GenbankMetadata.data", FileMode.Create);
BinaryFormatter formatter = new BinaryFormatter();
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(@"testdata\GenBank\NC_001284.gbk");
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
Assert.AreEqual(metadata.Features.All.Count, 743);
Assert.AreEqual(metadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(metadata.Features.Exons.Count, 32);
Assert.AreEqual(metadata.Features.Introns.Count, 22);
Assert.AreEqual(metadata.Features.Genes.Count, 60);
Assert.AreEqual(metadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(metadata.Features.Promoters.Count, 17);
Assert.AreEqual(metadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(metadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(metadata.Features.CodingSequences[0].Translation.Trim('"'), metadata.Features.CodingSequences[0].GetTranslation().ToString());
Assert.AreEqual(metadata.GetFeatures(11918, 12241).Count, 2);
formatter.Serialize(stream, metadata);
stream.Seek(0, SeekOrigin.Begin);
GenBankMetadata deserializedMetadata = (GenBankMetadata)formatter.Deserialize(stream);
Assert.AreNotSame(metadata, deserializedMetadata);
Assert.AreEqual(deserializedMetadata.Features.All.Count, 743);
Assert.AreEqual(deserializedMetadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(deserializedMetadata.Features.Exons.Count, 32);
Assert.AreEqual(deserializedMetadata.Features.Introns.Count, 22);
Assert.AreEqual(deserializedMetadata.Features.Genes.Count, 60);
Assert.AreEqual(deserializedMetadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(deserializedMetadata.Features.Promoters.Count, 17);
Assert.AreEqual(deserializedMetadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(deserializedMetadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(deserializedMetadata.Features.CodingSequences[0].Translation.Trim('"'), metadata.Features.CodingSequences[0].GetTranslation().ToString());
Assert.AreEqual(deserializedMetadata.GetFeatures(11918, 12241).Count, 2);
}
catch
{
Assert.Fail();
}
finally
{
if (stream != null)
{
stream.Close();
stream = null;
}
}
}
public void TestGenBankWhenParsingOne()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_singleProteinSeqGenBankFilename);
// test the non-metadata properties
Assert.IsTrue(seq.IsReadOnly);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual(MoleculeType.DNA, seq.MoleculeType);
Assert.AreEqual("SCU49845", seq.DisplayID);
Assert.AreEqual("SCU49845", seq.ID);
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
Assert.AreEqual(metadata.Locus.Strand, SequenceStrandType.None);
Assert.AreEqual("none", metadata.Locus.StrandTopology.ToString().ToLower());
Assert.AreEqual("PLN", metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse("21-JUN-1999"), metadata.Locus.Date);
Assert.AreEqual("1", metadata.Version.Version);
Assert.AreEqual("1293613", metadata.Version.GINumber);
// test that we're correctly putting all types of metadata in the right places
Assert.AreEqual(1, seq.Metadata.Count);
IList <CitationReference> referenceList = metadata.References;
Assert.AreEqual(3, referenceList.Count);
IList <FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(6, featureList.Count);
Assert.AreEqual(4, featureList[0].Qualifiers.Count);
Assert.AreEqual(5, featureList[1].Qualifiers.Count);
Assert.AreEqual(1, featureList[2].Qualifiers.Count);
// test the sequence string
string expected = @"GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGTTACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAACATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAGACGCGAAAAAAAAAGAACAACGCGTCATAGAACTTTTGGCAATTCGCGTCACAAATAAATTTTGGCAACTTATGTTTCCTCTTCGAGCAGTACTCGAGCCCTGTCTCAAGAATGTAATAATACCCATCGTAGGTATGGTTAAAGATAGCATCTCCACAACCTCAAAGCTCCTTGCCGAGAGTCGCCCTCCTTTGTCGAGTAATTTTCACTTTTCATATGAGAACTTATTTTCTTATTCTTTACTCTCACATCCTGTAGTGATTGACACTGCAACAGCCACCATCACTAGAAGAACAGAACAATTACTTAATAGAAAAATTATATCTTCCTCGAAACGATTTCCTGCTTCCAACATCTACGTATATCAAGAAGCATTCACTTACCATGACACAGCTTCAGATTTCATTATTGCTGACAGCTACTATATCACTACTCCATCTAGTAGTGGCCACGCCCTATGAGGCATATCCTATCGGAAAACAATACCCCCCAGTGGCAAGAGTCAATGAATCGTTTACATTTCAAATTTCCAATGATACCTATAAATCGTCTGTAGACAAGACAGCTCAAATAACATACAATTGCTTCGACTTACCGAGCTGGCTTTCGTTTGACTCTAGTTCTAGAACGTTCTCAGGTGAACCTTCTTCTGACTTACTATCTGATGCGAACACCACGTTGTATTTCAATGTAATACTCGAGGGTACGGACTCTGCCGACAGCACGTCTTTGAACAATACATACCAATTTGTTGTTACAAACCGTCCATCCATCTCGCTATCGTCAGATTTCAATCTATTGGCGTTGTTAAAAAACTATGGTTATACTAACGGCAAAAACGCTCTGAAACTAGATCCTAATGAAGTCTTCAACGTGACTTTTGACCGTTCAATGTTCACTAACGAAGAATCCATTGTGTCGTATTACGGACGTTCTCAGTTGTATAATGCGCCGTTACCCAATTGGCTGTTCTTCGATTCTGGCGAGTTGAAGTTTACTGGGACGGCACCGGTGATAAACTCGGCGATTGCTCCAGAAACAAGCTACAGTTTTGTCATCATCGCTACAGACATTGAAGGATTTTCTGCCGTTGAGGTAGAATTCGAATTAGTCATCGGGGCTCACCAGTTAACTACCTCTATTCAAAATAGTTTGATAATCAACGTTACTGACACAGGTAACGTTTCATATGACTTACCTCTAAACTATGTTTATCTCGATGACGATCCTATTTCTTCTGATAAATTGGGTTCTATAAACTTATTGGATGCTCCAGACTGGGTGGCATTAGATAATGCTACCATTTCCGGGTCTGTCCCAGATGAATTACTCGGTAAGAACTCCAATCCTGCCAATTTTTCTGTGTCCATTTATGATACTTATGGTGATGTGATTTATTTCAACTTCGAAGTTGTCTCCACAACGGATTTGTTTGCCATTAGTTCTCTTCCCAATATTAACGCTACAAGGGGTGAATGGTTCTCCTACTATTTTTTGCCTTCTCAGTTTACAGACTACGTGAATACAAACGTTTCATTAGAGTTTACTAATTCAAGCCAAGACCATGACTGGGTGAAATTCCAATCATCTAATTTAACATTAGCTGGAGAAGTGCCCAAGAATTTCGACAAGCTTTCATTAGGTTTGAAAGCGAACCAAGGTTCACAATCTCAAGAGCTATATTTTAACATCATTGGCATGGATTCAAAGATAACTCACTCAAACCACAGTGCGAATGCAACGTCCACAAGAAGTTCTCACCACTCCACCTCAACAAGTTCTTACACATCTTCTACTTACACTGCAAAAATTTCTTCTACCTCCGCTGCTGCTACTTCTTCTGCTCCAGCAGCGCTGCCAGCAGCCAATAAAACTTCATCTCACAATAAAAAAGCAGTAGCAATTGCGTGCGGTGTTGCTATCCCATTAGGCGTTATCCTAGTAGCTCTCATTTGCTTCCTAATATTCTGGAGACGCAGAAGGGAAAATCCAGACGATGAAAACTTACCGCATGCTATTAGTGGACCTGATTTGAATAATCCTGCAAATAAACCAAATCAAGAAAACGCTACACCTTTGAACAACCCCTTTGATGATGATGCTTCCTCGTACGATGATACTTCAATAGCAAGAAGATTGGCTGCTTTGAACACTTTGAAATTGGATAACCACTCTGCCACTGAATCTGATATTTCCAGCGTGGATGAAAAGAGAGATTCTCTATCAGGTATGAATACATACAATGATCAGTTCCAATCCCAAAGTAAAGAAGAATTATTAGCAAAACCCCCAGTACAGCCTCCAGAGAGCCCGTTCTTTGACCCACAGAATAGGTCTTCTTCTGTGTATATGGATAGTGAACCAGCAGTAAATAAATCCTGGCGATATACTGGCAACCTGTCACCAGTCTCTGATATTGTCAGAGACAGTTACGGATCACAAAAAACTGTTGATACAGAAAAACTTTTCGATTTAGAAGCACCAGAGAAGGAAAAACGTACGTCAAGGGATGTCACTATGTCTTCACTGGACCCTTGGAACAGCAATATTAGCCCTTCTCCCGTAAGAAAATCAGTAACACCATCACCATATAACGTAACGAAGCATCGTAACCGCCACTTACAAAATATTCAAGACTCTCAAAGCGGTAAAAACGGAATCACTCCCACAACAATGTCAACTTCATCTTCTGACGATTTTGTTCCGGTTAAAGATGGTGAAAATTTTTGCTGGGTCCATAGCATGGAACCAGACAGAAGACCAAGTAAGAAAAGGTTAGTAGATTTTTCAAATAAGAGTAATGTCAATGTTGGTCAAGTTAAGGACATTCACGGACGCATCCCAGAAATGCTGTGATTATACGCAACGATATTTTGCTTAATTTTATTTTCCTGTTTTATTTTTTATTAGTGGTTTACAGATACCCTATATTTTATTTAGTTTTTATACTTAGAGACATTTAATTTTAATTCCATTCTTCAAATTTCATTTTTGCACTTAAAACAAAGATCCAAAAATGCTCTCGCCCTCTTCATATTGAGAATACACTCCATTCAAAATTTTGTCGTCACCGCTGATTAATTTTTCACTAAACTGATGAATAATCAAAGGCCCCACGTCAGAACCGACTAAAGAAGTGAGTTTTATTTTAGGAGGTTGAAAACCATTATTGTCTGGTAAATTTTCATCTTCTTGACATTTAACCCAGTTTGAATCCCTTTCAATTTCTGCTTTTTCCTCCAAACTATCGACCCTCCTGTTTCTGTCCAACTTATGTCCTAGTTCCAATTCGATCGCATTAATAACTGCTTCAAATGTTATTGTGTCATCGTTGACTTTAGGTAATTTCTCCAAATGCATAATCAAACTATTTAAGGAAGATCGGAATTCGTCGAACACTTCAGTTTCCGTAATGATCTGATCGTCTTTATCCACATGTTGTAATTCACTAAAATCTAAAACGTATTTTTCAATGCATAAATCGTTCTTTTTATTAATAATGCAGATGGAAAATCTGTAAACGTGCGTTAATTTAGAAAGAACATCCAGTATAAGTTCTTCTATATAGTCAATTAAAGCAGGATGCCTATTAATGGGAACGAACTGCGGCAAGTTGAATGACTGGTAAGTAGTGTAGTCGAATGACTGAGGTGGGTATACATTTCTATAAAATAAAATCAAATTAATGTAGCATTTTAAGTATACCCTCAGCCACTTCTCTACCCATCTATTCATAAAGCTGACGCAACGATTACTATTTTTTTTTTCTTCTTGGATCTCAGTCGTCGCAAAAACGTATACCTTCTTTTTCCGACCTTTTTTTTAGCTTTCTGGAAAAGTTTATATTAGTTAAACAGGGTCTAGTCTTAGTGTGAAAGCTAGTGGTTTCGATTGACTGATATTAAGAAAGTGGAAATTAAATTAGTAGTGTAGACGTATATGCATATGTATTTCTCGCCTGTTTATGTTTCTACGTACTTTTGATTTATAGCAAGGGGAAAAGAAATACATACTATTTTTTGGTAAAGGTGAAAGCATAATGTAAAAGCTAGAATAAAATGGACGAAATAAAGAGAGGCTTAGTTCATCTTTTTTCCAAAAAGCACCCAATGATAATAACTAAAATGAAAAGGATTTGCCATCTGTCAGCAACATCAGTTGTGTGAGCAATAATAAAATCATCACCTCCGTTGCCTTTAGCGCGTTTGTCGTTTGTATCTTCCGTAATTTTAGTCTTATCAATGGGAATCATAAATTTTCCAATGAATTAGCAATTTCGTCCAATTCTTTTTGAGCTTCTTCATATTTGCTTTGGAATTCTTCGCACTTCTTTTCCCATTCATCTCTTTCTTCTTCCAAAGCAACGATCCTTCTACCCATTTGCTCAGAGTTCAAATCGGCCTCTTTCAGTTTATCCATTGCTTCCTTCAGTTTGGCTTCACTGTCTTCTAGCTGTTGTTCTAGATCCTGGTTTTTCTTGGTGTAGTTCTCATTATTAGATCTCAAGTTATTGGAGTCTTCAGCCAATTGCTTTGTATCAGACAATTGACTCTCTAACTTCTCCACTTCACTGTCGAGTTGCTCGTTTTTAGCGGACAAAGATTTAATCTCGTTTTCTTTTTCAGTGTTAGATTGCTCTAATTCTTTGAGCTGTTCTCTCAGCTCCTCATATTTTTCTTGCCATGACTCAGATTCTAATTTTAAGCTATTCAATTTCTCTTTGATC";
Assert.AreEqual(expected, seq.ToString());
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.ParseOne(_singleDnaSeqGenBankFilename);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
void InvalidateGenBankParser(string node)
{
// Initialization of xml strings.
FilePath = _utilityObj._xmlUtil.GetTextValue(node,
Constants.FilePathNode);
try
{
GenBankParser parserObj = new GenBankParser();
if (string.Equals(Constants.SimpleGenBankNodeName, node))
{
parserObj.LocationBuilder = null;
}
else if (string.Equals(Constants.SimpleGenBankPrimaryNode, node))
{
parserObj.Alphabet = Alphabets.RNA;
}
parserObj.ParseOne(FilePath);
Assert.Fail();
}
catch (InvalidOperationException)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
catch (Exception)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
}
public void TestGenBankWhenUserSetsIncorrectAlphabet()
{
// parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.Protein;
bool failed = false;
try
{
ISequence seq = parser.ParseOne(_singleDnaSeqGenBankFilename);
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for trying to create sequence using incorrect alphabet.");
}
}
public static int[] GetBestAnnotatedIndex(UIParameters Up, int seqPos)
{
// BLAST reports are saved in individual files by query and
// numbered in the same order as they appear in the input FASTA file.
int[] annotatedIndex = new int[2];
annotatedIndex[0] = -1;
annotatedIndex[1] = -1;
string blastFile = Up.ProjectDir + "\\xml\\" + seqPos + ".xml";
if (!File.Exists(blastFile))
{
throw new Exception("File does not exist.");
}
BlastXmlParser blastParser = new BlastXmlParser();
IList <BlastResult> blastResults = blastParser.Parse(blastFile);
GenBankParser gbParser = new GenBankParser();
// iterate through the BLAST results.
foreach (BlastResult blastResult in blastResults)
{
foreach (BlastSearchRecord record in blastResult.Records)
{
int hitsProcessed = 0;
// If there are not hits in the BLAST result ...
int rank = 0;
if (record.Hits.Count() > 0)
{
// For each hit
for (int i = 0; i < record.Hits.Count(); i++)
{
Hit blastHit = record.Hits[i];
for (int j = 0; j < blastHit.Hsps.Count(); j++)
{
Hsp blastHsp = blastHit.Hsps[j];
double percentId = (blastHsp.IdentitiesCount / (double)blastHsp.AlignmentLength) * 100;
double queryCoverage = ((double)(blastHsp.QueryEnd - blastHsp.QueryStart + 1) / record.IterationQueryLength) * 100;
if ((percentId >= Up.BlastMinPercentIdentity) &&
(Up.BlastMaxEvalue >= blastHsp.EValue) &&
(queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
(hitsProcessed < Up.BlastMaxNumHits))
{
rank += 1;
long gi = Convert.ToInt64(blastHit.Id.Split('|')[1]);
GenBankItem gitem = new GenBankItem(gi, blastHsp.HitStart, blastHsp.HitEnd);
string gbFile = Up.ProjectDir + "\\gb\\" + gitem.Id.ToString();
gbFile += "_" + gitem.HitStart.ToString();
gbFile += "_" + gitem.HitEnd.ToString();
gbFile += ".gb";
try
{
Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
ISequence gbRecord = gbParser.ParseOne(gbFile);
GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
IList <FeatureItem> features = gbMeta.Features.All;
FeatureItem bestItem = getBestFeatureItem(features);
if (bestItem != null)
{
annotatedIndex[0] = i;
annotatedIndex[1] = j;
return(annotatedIndex);
}
}
catch
{
Console.WriteLine("ISANNOTATED: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
}
hitsProcessed += 1;
}
}
}
}
}
}
return(annotatedIndex);
}
public void TestFeatureItem()
{
ISequence seq;
ISequence featureSeq = null;
GenBankParser parser = new GenBankParser();
string _genBankDataPath = @"TestUtils\GenBank";
seq = parser.ParseOne(_genBankDataPath + @"\BK000016-tpa.gbk");
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
#region Test GetSubSequence Method
featureSeq = metadata.Features.All[0].GetSubSequence(seq);
int start = metadata.Features.All[0].Location.Start - 1;
int end = metadata.Features.All[0].Location.End - start;
Assert.AreEqual(featureSeq.ToString(), seq.Range(start, end).ToString());
featureSeq = metadata.Features.All[1].GetSubSequence(seq);
start = metadata.Features.All[1].Location.Start - 1;
end = metadata.Features.All[1].Location.End - start;
Assert.AreEqual(featureSeq.ToString(), seq.Range(start, end).ToString());
seq = new Sequence(Alphabets.DNA, "ACGTAAAGGT");
Sequence refSeq = new Sequence(Alphabets.DNA, "AAAAATTTT");
LocationBuilder locbuilder = new LocationBuilder();
ILocation loc = locbuilder.GetLocation("join(complement(4..8),Ref1:5..7)");
Assert.AreEqual("join(complement(4..8),Ref1:5..7)", locbuilder.GetLocationString(loc));
FeatureItem fi = new FeatureItem("Feature1", loc);
Dictionary <string, ISequence> refSeqs = new Dictionary <string, ISequence>();
refSeqs.Add("Ref1", refSeq);
ISequence result = fi.GetSubSequence(seq, refSeqs);
Assert.AreEqual("ATTTCATT", result.ToString());
#endregion
#region Test GetSubFeatures Method
SequenceFeatures seqFeatures = new SequenceFeatures();
FeatureItem source = new FeatureItem("Source", "1..1509");
FeatureItem mRNA = new FeatureItem("mRNA", "join(10..567,789..1320)");
FeatureItem cds = new FeatureItem("CDS", "join(54..567,789..1254)");
FeatureItem exon1 = new FeatureItem("Exon", "10..567");
FeatureItem intron = new FeatureItem("Intron", "568..788");
FeatureItem exon2 = new FeatureItem("Exon", "789..1320");
seqFeatures.All.Add(source);
seqFeatures.All.Add(mRNA);
seqFeatures.All.Add(cds);
seqFeatures.All.Add(exon1);
seqFeatures.All.Add(intron);
seqFeatures.All.Add(exon2);
List <FeatureItem> subFeatures = source.GetSubFeatures(seqFeatures);
Assert.AreEqual(5, subFeatures.Count);
subFeatures = mRNA.GetSubFeatures(seqFeatures);
Assert.AreEqual(4, subFeatures.Count);
subFeatures = cds.GetSubFeatures(seqFeatures);
Assert.AreEqual(1, subFeatures.Count);
subFeatures = exon1.GetSubFeatures(seqFeatures);
Assert.AreEqual(0, subFeatures.Count);
subFeatures = intron.GetSubFeatures(seqFeatures);
Assert.AreEqual(0, subFeatures.Count);
subFeatures = exon2.GetSubFeatures(seqFeatures);
Assert.AreEqual(0, subFeatures.Count);
#endregion
}
public static int CreateItems(UIParameters Up, ISequence rec, int itemId, int seqPos, Collection collection)
{
string queryName = rec.DisplayID.ToString().Split(' ')[0];
// BLAST reports are saved in individual files by query and
// numbered in the same order as they appear in the input FASTA file.
string blastFile = Up.ProjectDir + "\\xml\\" + seqPos + ".xml";
if (!File.Exists(blastFile))
{
throw new Exception("File does not exist.");
}
BlastXmlParser blastParser = new BlastXmlParser();
IList<BlastResult> blastResults = blastParser.Parse(blastFile);
GenBankParser gbParser = new GenBankParser();
int[] annotatedIndex = GetBestAnnotatedIndex(Up, seqPos);
// iterate through the BLAST results.
foreach (BlastResult blastResult in blastResults)
{
foreach (BlastSearchRecord record in blastResult.Records)
{
int hitsProcessed = 0;
// If there are not hits in the BLAST result ...
int rank = 0;
if (record.Hits.Count() > 0)
{
// For each hit
for (int i = 0; i < record.Hits.Count(); i++)
{
Hit blastHit = record.Hits[i];
// For each HSP
for (int j = 0; j < blastHit.Hsps.Count(); j++)
{
Hsp blastHsp = blastHit.Hsps[j];
double percentId = (blastHsp.IdentitiesCount / (double)blastHsp.AlignmentLength) * 100;
double queryCoverage = ((double)(blastHsp.QueryEnd - blastHsp.QueryStart + 1) / record.IterationQueryLength) * 100;
string txt = String.Format("{0} {1} {2} {3} {4} {5} {6} {7}", percentId, Up.BlastMinPercentIdentity,
Up.BlastMaxEvalue, blastHsp.EValue, queryCoverage, Up.BlastMinPercentQueryCoverage,
hitsProcessed, Up.BlastMaxNumHits);
// if HSP passes user-defined thresholds
if ((percentId >= Up.BlastMinPercentIdentity) &&
(Up.BlastMaxEvalue >= blastHsp.EValue) &&
(queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
(hitsProcessed < Up.BlastMaxNumHits))
{
rank += 1;
string nextScore = "no";
if ((i + 1) < record.Hits.Count())
{
if (blastHsp.Score > record.Hits[i + 1].Hsps[0].Score)
{
nextScore = "less than";
}
else
{
nextScore = "equal";
}
}
else
{
nextScore = "non existent";
}
// parse GI numner from hit
long gi = Convert.ToInt64(blastHit.Id.Split('|')[1]);
GenBankItem gitem = new GenBankItem(gi, blastHsp.HitStart, blastHsp.HitEnd);
string gbFile = Up.ProjectDir + "\\gb\\" + gitem.Id.ToString();
gbFile += "_" + gitem.HitStart.ToString();
gbFile += "_" + gitem.HitEnd.ToString();
gbFile += ".gb";
// init item
string img = "#" + itemId.ToString();
Item item = new Item(itemId, img);
string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
item.Name = headerTokens[0];
item.Description = headerTokens[1];
// write pairwise alignment
writePairwiseAlignment(Up, blastHit, j, itemId);
// try to parse the GB record associated with the hit and set facet values to data from BLAST/GB record
try
{
Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
ISequence gbRecord = gbParser.ParseOne(gbFile);
item.Href = GetNCBIUrl(Up.BlastProgram) + GetGenBankIdentifier(gbRecord);
GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
CodingSequence bestCds = null;
IList<FeatureItem> features = gbMeta.Features.All;
FeatureItem bestItem = getBestFeatureItem(features);
if (gbMeta.Features.CodingSequences.Count > 0)
{
bestCds = gbMeta.Features.CodingSequences[0];
}
for (int k = 1; k < gbMeta.Features.CodingSequences.Count; k++)
{
CodingSequence cds = gbMeta.Features.CodingSequences[k];
//int bestSize = Math.Abs(bestCds.Location.End - bestCds.Location.Start);
int bestSize = Math.Abs(bestItem.Location.End - bestItem.Location.Start);
int cdsSize = Math.Abs(cds.Location.End - cds.Location.Start);
if (cdsSize > bestSize)
{
bestCds = cds;
}
}
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case "InputOrder":
facet = new Facet(f.Name, f.Type, seqPos);
break;
case "QuerySequence":
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
case "NextScore":
facet = new Facet(f.Name, f.Type, nextScore);
break;
case "Annotated":
string value = "na";
if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
{
value = "top_annotated";
}
else
{
if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
{
value = "top_unannotated";
}else{
if (bestItem != null)
{
value = "annotated";
}else{
value = "unannotated";
}
}
}
facet = new Facet(f.Name, f.Type, value);
break;
default:
//facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestCds, rank);
facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestItem, rank);
break;
}
/*
if (f.Name == "InputOrder")
{
facet = new Facet(f.Name, f.Type, seqPos);
}
else
{
facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item);
}
*/
item.Facets.Add(facet);
}
}
//catch (System.NullReferenceException e) // if parsing failed init the item w/ default values (similar to 'no hit' above)
catch
{
Console.WriteLine("GB ERROR: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
item.Href = "#";
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case ("InputOrder"):
facet = new Facet(f.Name, f.Type, seqPos);
break;
case "QuerySequence":
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
case ("NextScore"):
facet = new Facet(f.Name, f.Type, "no");
break;
case "Annotated":
string value = "na";
if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
{
value = "top_annotated";
}
else
{
if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
{
value = "top_unannotated";
}
else
{
value = "unannotated";
}
}
facet = new Facet(f.Name, f.Type, value);
break;
default:
facet = CreateGBErrorFacet(f.Name, f.Type, record, i, j, item, GetNCBIUrl(Up.BlastProgram), rank);
break;
}
item.Facets.Add(facet);
}
//throw (e);
}
// Add item to collection, increment to next item,
collection.Items.Add(item);
hitsProcessed += 1;
itemId += 1;
}
}
}
}
if ((record.Hits.Count()) == 0 || (hitsProcessed == 0))
{
// Init Pivot item
string img = "#" + itemId.ToString();
Item item = new Item(itemId, img);
item.Href = "#";
string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
item.Name = headerTokens[0];
item.Description = headerTokens[1];
// Write pairwise alignment to file.
writePairwiseAlignment(Up, itemId);
// Set facet values for each facet category to default values
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case ("InputOrder"):
facet = new Facet(f.Name, f.Type, seqPos);
break;
case ("QuerySequence"):
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
default:
facet = CreateFacet(f.Name, f.Type, record, item, 0);
break;
}
item.Facets.Add(facet);
}
// Add item to collection, increment to next item, skip remaining code
collection.Items.Add(item);
itemId += 1;
hitsProcessed += 1;
}
}
}
return itemId;
}
public static int CreateItems(UIParameters Up, ISequence rec, int itemId, int seqPos, Collection collection)
{
string queryName = rec.DisplayID.ToString().Split(' ')[0];
// BLAST reports are saved in individual files by query and
// numbered in the same order as they appear in the input FASTA file.
string blastFile = Up.ProjectDir + "\\xml\\" + seqPos + ".xml";
if (!File.Exists(blastFile))
{
throw new Exception("File does not exist.");
}
BlastXmlParser blastParser = new BlastXmlParser();
IList <BlastResult> blastResults = blastParser.Parse(blastFile);
GenBankParser gbParser = new GenBankParser();
int[] annotatedIndex = GetBestAnnotatedIndex(Up, seqPos);
// iterate through the BLAST results.
foreach (BlastResult blastResult in blastResults)
{
foreach (BlastSearchRecord record in blastResult.Records)
{
int hitsProcessed = 0;
// If there are not hits in the BLAST result ...
int rank = 0;
if (record.Hits.Count() > 0)
{
// For each hit
for (int i = 0; i < record.Hits.Count(); i++)
{
Hit blastHit = record.Hits[i];
// For each HSP
for (int j = 0; j < blastHit.Hsps.Count(); j++)
{
Hsp blastHsp = blastHit.Hsps[j];
double percentId = (blastHsp.IdentitiesCount / (double)blastHsp.AlignmentLength) * 100;
double queryCoverage = ((double)(blastHsp.QueryEnd - blastHsp.QueryStart + 1) / record.IterationQueryLength) * 100;
string txt = String.Format("{0} {1} {2} {3} {4} {5} {6} {7}", percentId, Up.BlastMinPercentIdentity,
Up.BlastMaxEvalue, blastHsp.EValue, queryCoverage, Up.BlastMinPercentQueryCoverage,
hitsProcessed, Up.BlastMaxNumHits);
// if HSP passes user-defined thresholds
if ((percentId >= Up.BlastMinPercentIdentity) &&
(Up.BlastMaxEvalue >= blastHsp.EValue) &&
(queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
(hitsProcessed < Up.BlastMaxNumHits))
{
rank += 1;
string nextScore = "no";
if ((i + 1) < record.Hits.Count())
{
if (blastHsp.Score > record.Hits[i + 1].Hsps[0].Score)
{
nextScore = "less than";
}
else
{
nextScore = "equal";
}
}
else
{
nextScore = "non existent";
}
// parse GI numner from hit
long gi = Convert.ToInt64(blastHit.Id.Split('|')[1]);
GenBankItem gitem = new GenBankItem(gi, blastHsp.HitStart, blastHsp.HitEnd);
string gbFile = Up.ProjectDir + "\\gb\\" + gitem.Id.ToString();
gbFile += "_" + gitem.HitStart.ToString();
gbFile += "_" + gitem.HitEnd.ToString();
gbFile += ".gb";
// init item
string img = "#" + itemId.ToString();
Item item = new Item(itemId, img);
string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
item.Name = headerTokens[0];
item.Description = headerTokens[1];
// write pairwise alignment
writePairwiseAlignment(Up, blastHit, j, itemId);
// try to parse the GB record associated with the hit and set facet values to data from BLAST/GB record
try
{
Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
ISequence gbRecord = gbParser.ParseOne(gbFile);
item.Href = GetNCBIUrl(Up.BlastProgram) + GetGenBankIdentifier(gbRecord);
GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
CodingSequence bestCds = null;
IList <FeatureItem> features = gbMeta.Features.All;
FeatureItem bestItem = getBestFeatureItem(features);
if (gbMeta.Features.CodingSequences.Count > 0)
{
bestCds = gbMeta.Features.CodingSequences[0];
}
for (int k = 1; k < gbMeta.Features.CodingSequences.Count; k++)
{
CodingSequence cds = gbMeta.Features.CodingSequences[k];
//int bestSize = Math.Abs(bestCds.Location.End - bestCds.Location.Start);
int bestSize = Math.Abs(bestItem.Location.End - bestItem.Location.Start);
int cdsSize = Math.Abs(cds.Location.End - cds.Location.Start);
if (cdsSize > bestSize)
{
bestCds = cds;
}
}
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case "InputOrder":
facet = new Facet(f.Name, f.Type, seqPos);
break;
case "QuerySequence":
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
case "NextScore":
facet = new Facet(f.Name, f.Type, nextScore);
break;
case "Annotated":
string value = "na";
if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
{
value = "top_annotated";
}
else
{
if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
{
value = "top_unannotated";
}
else
{
if (bestItem != null)
{
value = "annotated";
}
else
{
value = "unannotated";
}
}
}
facet = new Facet(f.Name, f.Type, value);
break;
default:
//facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestCds, rank);
facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item, GetNCBIUrl(Up.BlastProgram), bestItem, rank);
break;
}
/*
* if (f.Name == "InputOrder")
* {
* facet = new Facet(f.Name, f.Type, seqPos);
* }
*
* else
* {
* facet = CreateFacet(f.Name, f.Type, record, i, j, gbRecord, item);
* }
*/
item.Facets.Add(facet);
}
}
//catch (System.NullReferenceException e) // if parsing failed init the item w/ default values (similar to 'no hit' above)
catch
{
Console.WriteLine("GB ERROR: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
item.Href = "#";
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case ("InputOrder"):
facet = new Facet(f.Name, f.Type, seqPos);
break;
case "QuerySequence":
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
case ("NextScore"):
facet = new Facet(f.Name, f.Type, "no");
break;
case "Annotated":
string value = "na";
if ((annotatedIndex[0] == i) && (annotatedIndex[1] == j))
{
value = "top_annotated";
}
else
{
if ((i == 0) && (j == 0) && (annotatedIndex[0] == -1) && (annotatedIndex[1] == -1))
{
value = "top_unannotated";
}
else
{
value = "unannotated";
}
}
facet = new Facet(f.Name, f.Type, value);
break;
default:
facet = CreateGBErrorFacet(f.Name, f.Type, record, i, j, item, GetNCBIUrl(Up.BlastProgram), rank);
break;
}
item.Facets.Add(facet);
}
//throw (e);
}
// Add item to collection, increment to next item,
collection.Items.Add(item);
hitsProcessed += 1;
itemId += 1;
}
}
}
}
if ((record.Hits.Count()) == 0 || (hitsProcessed == 0))
{
// Init Pivot item
string img = "#" + itemId.ToString();
Item item = new Item(itemId, img);
item.Href = "#";
string[] headerTokens = parseFastaHeader(rec.DisplayID.ToString());
item.Name = headerTokens[0];
item.Description = headerTokens[1];
// Write pairwise alignment to file.
writePairwiseAlignment(Up, itemId);
// Set facet values for each facet category to default values
foreach (FacetCategory f in Up.FacetCategories)
{
Facet facet = new Facet();
switch (f.Name)
{
case ("InputOrder"):
facet = new Facet(f.Name, f.Type, seqPos);
break;
case ("QuerySequence"):
facet = new Facet(f.Name, f.Type, rec.ToString());
break;
default:
facet = CreateFacet(f.Name, f.Type, record, item, 0);
break;
}
item.Facets.Add(facet);
}
// Add item to collection, increment to next item, skip remaining code
collection.Items.Add(item);
itemId += 1;
hitsProcessed += 1;
}
}
}
return(itemId);
}
private void DoGenBank()
{
int progValue = 0;
Dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Normal, new Action(delegate()
{
(CurrentControl as UserControl5).UserControl5Step1.Foreground = System.Windows.Media.Brushes.Black;
progressBar1.Value = progValue;
}));
string inputDir = Up.ProjectDir + "\\xml";
if (!Directory.Exists(inputDir))
{
throw new Exception("Directory " + inputDir + " does not exist.");
}
string[] blastXmlFiles = Directory.GetFiles(inputDir, "*.xml");
int c = 1;
Stack<GenBankItem> giList = new Stack<GenBankItem>();
foreach (string blastFile in blastXmlFiles)
{
BlastXmlParser blastParser = new BlastXmlParser();
progValue = Convert.ToInt32(Math.Round((double)c / blastXmlFiles.Count() * 100, 0));
UpdateProgressBar(progValue, "Filtering results");
try
{
IList<BlastResult> blastResults = blastParser.Parse(blastFile);
List<GenBankItem> recordGiList = BlastUtil.filter(blastResults, Up.BlastMaxNumHits, Up.BlastMaxEvalue, Up.BlastMinPercentIdentity, Up.BlastMinPercentQueryCoverage);
foreach (GenBankItem gi in recordGiList)
{
giList.Push(gi);
Debug.WriteLine(gi.HitStart.ToString() + " " + gi.HitEnd.ToString());
}
}
catch
{
FatalErrorDialog("Cannot parse " + blastFile);
Debug.WriteLine("Cannot parse " + blastFile);
}
c += 1;
}
progValue = 0;
Dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Normal, new Action(delegate()
{
(CurrentControl as UserControl5).UserControl5Step2.Foreground = System.Windows.Media.Brushes.Black;
progressBar1.Value = progValue;
}));
int totalGi = giList.Count();
GenBankParser genkBankParser = new GenBankParser();
int unParsableCount = 0;
int notDownloadedCount = 0;
string unParsableGIs = "";
string notDownloadedGIs = "";
bool isConnected = true;
if (!IsConnectedToInternet())
{
isConnected = false;
MessageBox.Show("Your internet connection appears to be down. As a result, missing GenBank records will not be downloaded.");
}
while (giList.Count > 0)
{
GenBankItem gitem = giList.Pop();
progValue = Convert.ToInt32(Math.Round(((totalGi - giList.Count()) / (double)totalGi) * 100, 0));
UpdateProgressBar(progValue, "Downloading GenBank records");
string outFilename = Up.ProjectDir + "\\gb\\" + gitem.Id;
outFilename += "_" + gitem.HitStart.ToString();
outFilename += "_" + gitem.HitEnd.ToString();
outFilename += ".gb";
WebClient wc = new WebClient();
if (File.Exists(outFilename))
{
try
{
ISequence gpitem = genkBankParser.ParseOne(outFilename);
}
catch
{
if (isConnected)
{
string url = GetGenbankUrl(gitem);
try
{
wc.DownloadFile(url, outFilename);
Thread.Sleep(1000);
}
catch
{
wc.Proxy = null;
giList.Push(gitem);
}
try
{
ISequence gpitem = genkBankParser.ParseOne(outFilename);
}
catch
{
unParsableCount += 1;
unParsableGIs += gitem.Id + ",";
}
}
else
{
notDownloadedCount += 1;
notDownloadedGIs += gitem.Id + ",";
}
}
}
else
{
if (isConnected)
{
string url = GetGenbankUrl(gitem);
try
{
wc.DownloadFile(url, outFilename);
Thread.Sleep(1000);
}
catch
{
wc.Proxy = null;
giList.Push(gitem);
}
try
{
ISequence gpitem = genkBankParser.ParseOne(outFilename);
}
catch
{
unParsableCount += 1;
unParsableGIs += gitem.Id + ",";
}
}
else
{
notDownloadedCount += 1;
notDownloadedGIs += gitem.Id + ",";
}
}
}
if (notDownloadedCount > 0)
{
MessageBox.Show("Error downloading GenBank records: " + notDownloadedGIs + ".\r\nThis is likely caused by an interruption in the internet connection. Re-attempt the download by repeating this step.\r\n");
}
if (unParsableCount > 0)
{
MessageBox.Show("Error parsing GenBank records: " + unParsableGIs + ".\r\nThis is likely due to an unsupported field in the GenBank record. Contact the MBF development team at http://mbf.codeplex.com, and include one of the GI numbers in the bug report.\r\nYou can copy this message to the clipboard using Ctrl-C.\r\n");
}
}
public void GenBankParserValidateParseOneWithSpecificFormats()
{
InitializeXmlVariables();
// Initialization of xml strings.
FilePath = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.FilePathNode);
AlphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.AlphabetNameNode);
MolType = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.MoleculeTypeNode);
IsSequenceReadOnly = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.IsReadOnlyNode);
SeqId = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.SequenceIdNode);
StrandTopology = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.StrandTopologyNode);
StrandType = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.StrandTypeNode);
Div = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.DivisionNode);
Version = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.VersionNode);
SequenceDate = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.DateNode);
PrimaryId = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.PrimaryIdNode);
ExpectedSequence = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.ExpectedSequenceNode);
// parse
BasicSequenceParser parserObj = new GenBankParser();
parserObj.Alphabet = Alphabets.Protein;
parserObj.Encoding = NcbiEAAEncoding.Instance;
ISequence seq = parserObj.ParseOne(FilePath);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName),
seq.Alphabet);
Assert.AreEqual(Utility.GetMoleculeType(MolType),
seq.MoleculeType);
Assert.AreEqual(SeqId, seq.DisplayID);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(
CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GINumber);
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, seq.ToString());
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Parser BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
}
public static int[] GetBestAnnotatedIndex(UIParameters Up, int seqPos)
{
// BLAST reports are saved in individual files by query and
// numbered in the same order as they appear in the input FASTA file.
int[] annotatedIndex = new int[2];
annotatedIndex[0] = -1;
annotatedIndex[1] = -1;
string blastFile = Up.ProjectDir + "\\xml\\" + seqPos + ".xml";
if (!File.Exists(blastFile))
{
throw new Exception("File does not exist.");
}
BlastXmlParser blastParser = new BlastXmlParser();
IList<BlastResult> blastResults = blastParser.Parse(blastFile);
GenBankParser gbParser = new GenBankParser();
// iterate through the BLAST results.
foreach (BlastResult blastResult in blastResults)
{
foreach (BlastSearchRecord record in blastResult.Records)
{
int hitsProcessed = 0;
// If there are not hits in the BLAST result ...
int rank = 0;
if (record.Hits.Count() > 0)
{
// For each hit
for (int i = 0; i < record.Hits.Count(); i++)
{
Hit blastHit = record.Hits[i];
for (int j = 0; j < blastHit.Hsps.Count(); j++)
{
Hsp blastHsp = blastHit.Hsps[j];
double percentId = (blastHsp.IdentitiesCount / (double)blastHsp.AlignmentLength) * 100;
double queryCoverage = ((double)(blastHsp.QueryEnd - blastHsp.QueryStart + 1) / record.IterationQueryLength) * 100;
if ((percentId >= Up.BlastMinPercentIdentity) &&
(Up.BlastMaxEvalue >= blastHsp.EValue) &&
(queryCoverage >= Up.BlastMinPercentQueryCoverage) &&
(hitsProcessed < Up.BlastMaxNumHits))
{
rank += 1;
long gi = Convert.ToInt64(blastHit.Id.Split('|')[1]);
GenBankItem gitem = new GenBankItem(gi, blastHsp.HitStart, blastHsp.HitEnd);
string gbFile = Up.ProjectDir + "\\gb\\" + gitem.Id.ToString();
gbFile += "_" + gitem.HitStart.ToString();
gbFile += "_" + gitem.HitEnd.ToString();
gbFile += ".gb";
try
{
Console.WriteLine("GB OK: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
ISequence gbRecord = gbParser.ParseOne(gbFile);
GenBankMetadata gbMeta = (GenBankMetadata)gbRecord.Metadata["GenBank"];
IList<FeatureItem> features = gbMeta.Features.All;
FeatureItem bestItem = getBestFeatureItem(features);
if (bestItem != null)
{
annotatedIndex[0] = i;
annotatedIndex[1] = j;
return annotatedIndex;
}
}
catch
{
Console.WriteLine("ISANNOTATED: " + record.Hits[0].Id + " " + i.ToString() + " " + j.ToString());
}
hitsProcessed += 1;
}
}
}
}
}
}
return annotatedIndex;
}