public void ParseBlastValidation()
{
var blastFilePath = @"TestUtils\BlastRecords.xml";
var expectedGapCost = "11";
var expectedParameterMatrix = "BLOSUM62";
var expectedResultCount = "9";
var expectedDatabselength = "2974038";
var expectedHitsCount = "1";
var expectedAccession = "NP_010143";
var expectedAlignmentLength = "142";
var expectedBitScore = "33.113";
var expectedHitSequence = "KKIRKRCLAFPISQQIEMKTNIKNAGKLDNNNSPIVQDDS-----HNIIDVDGFLENQIQSNDHMIAADKGSGSLVNIIDTAPLTSTEFKPVEHPPVNY---------------VDLGNGLGLNTYNRGPPSIISDSTDEFY";
// Parse a Blast xml file.
BlastXmlParser parser = new BlastXmlParser();
IList <BlastResult> blastResults = parser.Parse(blastFilePath);
// Validate Meta data
BlastXmlMetadata meta = blastResults[0].Metadata;
Assert.AreEqual(meta.ParameterGapOpen.ToString((IFormatProvider)null),
expectedGapCost);
Assert.AreEqual(meta.ParameterMatrix.ToString((IFormatProvider)null),
expectedParameterMatrix);
// Validate blast records.
BlastSearchRecord record = blastResults[4].Records[0];
Assert.AreEqual(expectedResultCount, blastResults.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedDatabselength,
record.Statistics.DatabaseLength.ToString((IFormatProvider)null));
Assert.AreEqual(expectedHitsCount, record.Hits.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedAccession, record.Hits[0].Accession.ToString((IFormatProvider)null));
Assert.AreEqual(expectedHitsCount, record.Hits[0].Hsps.Count.ToString((IFormatProvider)null));
// Validate bit score.
Hsp highScoreSgment = record.Hits[0].Hsps[0];
Assert.AreEqual(expectedAlignmentLength, highScoreSgment.AlignmentLength.ToString(
(IFormatProvider)null));
Assert.AreEqual(expectedBitScore, highScoreSgment.BitScore.ToString((
IFormatProvider)null));
Assert.AreEqual(expectedHitSequence, highScoreSgment.HitSequence.ToString(
(IFormatProvider)null));
}
public void InValidateBlastXmlMetadataGetObjectData()
{
SerializationInfo info = null;
StreamingContext context = new StreamingContext(StreamingContextStates.All);
BlastXmlMetadata bxmObj = new BlastXmlMetadata();
try
{
bxmObj.GetObjectData(info, context);
Assert.Fail();
}
catch (ArgumentNullException)
{
Console.WriteLine("Ncbi Blast P2 : InValidated the GetObjectData() method successfully.");
ApplicationLog.WriteLine("Ncbi Blast P2 : InValidated the GetObjectData() method successfully.");
}
}
/// <summary>
/// Initializes a new instance of the BlastHeader class.
/// </summary>
/// <param name="metadata">BlastXmlMetadata instance.</param>
public BlastHeader(BlastXmlMetadata metadata)
{
this.InitializeComponent();
// Display Metadata information.
this.txtReference.Text = metadata.Reference;
this.txtVersion.Text = metadata.Version;
this.txtRid.Text = metadata.QueryId;
this.txtQuery.Text = metadata.QueryLength + " " + Properties.Resource.HEADER_LETTER;
this.txtDatabase.Text = metadata.Database;
// Initialize hyperlinks.
this.linkFaq.Click += new RoutedEventHandler(this.OnHyperLinkClicked);
this.linkFaq.NavigateUri = new Uri(Properties.Resource.FAQ_LINK);
this.linkTaxonomy.Click += new RoutedEventHandler(this.OnHyperLinkClicked);
this.linkTaxonomy.NavigateUri = new Uri(Properties.Resource.TAXONAMY_LINK);
this.KeyUp += new System.Windows.Input.KeyEventHandler(OnDialogKeyUp);
this.Owner = Application.Current.MainWindow;
}
protected void butBLAST_Click(object sender, EventArgs e)
{
string baseDir = ConfigurationManager.AppSettings["BLASTbase"];
string exomeRef = ConfigurationManager.AppSettings["RefName"];
string file = baseDir + @"temp\test" + DateTime.Now.ToString("yyyyMMddhhmmss");
string ls = Environment.NewLine.Normalize();
if (!txtBlast.Text.StartsWith(">"))
{
txtBlast.Text = @">No definition line" + ls + txtBlast.Text;
}
using (MemoryStream mstrm = new MemoryStream(Encoding.UTF8.GetBytes(txtBlast.Text))) {
ISequenceParser parser = SequenceParsers.Fasta;
ISequenceFormatter formatter = SequenceFormatters.Fasta;
try {
Sequence seq = (Sequence)parser.ParseOne(mstrm);
formatter.Format(seq, file + ".in");
txtBlast.Text = @">" + seq.ID + ls + seq.ConvertToString(0);
ErrorMessage.Text = "";
} catch (Exception ex) {
ErrorMessage.Text = ex.Message;
txtRes.Text = "";
return;
}
parser.Close();
formatter.Close();
}
Session["blast"] = txtBlast.Text;
using (Process blast = new Process()) {
blast.StartInfo.FileName = baseDir + @"bin\blastn.exe";
blast.StartInfo.UseShellExecute = false;
blast.StartInfo.Arguments = @"-task blastn -db " + baseDir + @"db\" + exomeRef + " -evalue 0.1 -outfmt 11 -query " + file + ".in -out " + file + ".asn -max_target_seqs 5";
blast.Start();
blast.WaitForExit();
}
if (File.Exists(file + ".asn"))
{
using (Process form = new Process()) {
form.StartInfo.FileName = baseDir + @"bin\blast_formatter.exe";
form.StartInfo.UseShellExecute = false;
form.StartInfo.Arguments = @"-archive " + file + ".asn" + @" -outfmt 5 -out " + file + ".xml";
form.Start();
form.WaitForExit();
form.StartInfo.Arguments = @"-archive " + file + ".asn" + @" -outfmt 0 -out " + file + ".txt";
form.Start();
form.WaitForExit();
}
using (StreamReader sr = new StreamReader(file + ".xml")) {
IBlastParser blastParser = new BlastXmlParser();
List <BlastResult> blastres = blastParser.Parse(sr.BaseStream).ToList();
ChartArea area = chartBlast.ChartAreas.FindByName("ChartArea1");
if (blastres.Count > 0)
{
BlastXmlMetadata meta = blastres[0].Metadata;
chartBlast.Titles.FindByName("blastTitle").Text = meta.QueryDefinition;
area.AxisY.Maximum = Math.Floor(meta.QueryLength + 5.0);
Series series = chartBlast.Series["Series1"];
series.Points.Clear();
int i = 0;
List <BlastHit> blasts = new List <BlastHit>();
chartBlast.Height = 30 * blastres[0].Records[0].Hits.Count + 50;
foreach (Hit hit in blastres[0].Records[0].Hits)
{
string contig = hit.Def;
for (int j = 0; j < hit.Hsps.Count; j++)
{
Hsp hsp = hit.Hsps[j];
int k = series.Points.AddXY(i, hsp.QueryStart, hsp.QueryEnd);
if (j < 1)
{
series.Points[k].Label = contig;
}
BlastHit bhit = new BlastHit();
bhit.seqID = Convert.ToInt64(hit.Accession);
bhit.Contig = contig;
bhit.Descr = hit.Def;
bhit.Score = hsp.BitScore.ToString("N2");
bhit.Evalue = hsp.EValue.ToString("E2");
bhit.HitStart = hsp.HitStart.ToString();
bhit.HitEnd = hsp.HitEnd.ToString();
bhit.Align = hsp.AlignmentLength.ToString();
bhit.Frame = hsp.QueryFrame > 0?"+":"-";
bhit.Frame += @"/";
bhit.Frame += hsp.HitFrame > 0 ? "+" : "-";
blasts.Add(bhit);
}
i++;
}
gridBLAST.DataSource = blasts;
}
else
{
gridBLAST.DataSource = null;
chartBlast.Height = 1;
}
gridBLAST.DataBind();
}
using (StreamReader sr = new StreamReader(file + ".txt", Encoding.UTF8, true)) {
txtRes.Text = sr.ReadToEnd();
}
}
else
{
txtRes.Text = "Nothing found.";
}
string[] tmpFiles = Directory.GetFiles(baseDir + @"temp\");
foreach (string filePath in tmpFiles)
{
if (File.GetLastWriteTime(filePath).CompareTo(DateTime.Now.AddDays(-28)) < 0)
{
File.Delete(filePath);
}
}
}
