/// <summary>
/// When implemented in a derived class, performs the execution of the activity.
/// </summary>
/// <param name="context">The execution context under which the activity executes.</param>
protected override void Execute(CodeActivityContext context)
{
string filename = Filename.Get(context);
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(filename);
if (formatter == null)
{
throw new ArgumentException("Could not determine formatter for " + filename);
}
if (LogOutput)
{
var tw = context.GetExtension <TextWriter>() ?? Console.Out;
tw.WriteLine("Writing sequences to " + filename);
}
try
{
foreach (var s in Sequences.Get(context))
{
formatter.Format(s);
}
}
finally
{
formatter.Close();
}
}
/// <summary>
/// Save in one of .NET Bio supported formats like fasta or GenBank.
/// </summary>
/// <param name="path">Filename.</param>
public void SaveAsBio(String path)
{
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(path);
formatter.Write(this.Sequence);
formatter.Close();
}
private void saveButton_Click(object sender, RoutedEventArgs e)
{
if (sequenceTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveSequenceFileDialog.ShowDialog() == true)
{
try
{
Fragment toSave = new Fragment();
toSave.Name = sequenceName;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequence);
toSave.Sequence = seq;
toSave.Length = sequence.Length;
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
//toSave.Construct.SaveAsBio(saveSequenceFileDialog.FileName);
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
static void Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine("Need source and destination filenames.");
return;
}
string sourceFilename = args[0];
string destFilename = args[1];
ISequenceParser parser = SequenceParsers.FindParserByFileName(sourceFilename);
if (parser == null)
{
parser = SequenceParsers.All.FirstOrDefault(
sp => sp.SupportedFileTypes.Contains(Path.GetExtension(sourceFilename)));
if (parser == null)
{
Console.WriteLine("Failed to locate parser for {0}", sourceFilename);
return;
}
parser.Open(sourceFilename);
}
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(destFilename);
if (formatter == null)
{
formatter = SequenceFormatters.All.FirstOrDefault(
sp => sp.SupportedFileTypes.Contains(Path.GetExtension(destFilename)));
if (formatter == null)
{
Console.WriteLine("Failed to locate formatter for {0}", destFilename);
return;
}
formatter.Open(destFilename);
}
foreach (var sequence in parser.Parse())
{
formatter.Write(sequence);
}
parser.Close();
formatter.Close();
}
/// <summary>
/// convert input file to output file using the specified format conversion
/// </summary>
public void ConvertFile()
{
//make sure input file is valid
if (!File.Exists(this.InputFile))
{
throw new Exception("Input file does not exist.");
}
//Finds a parser and opens the file
ISequenceParser inputParser = SequenceParsers.FindParserByFileName(this.InputFile);
if (inputParser == null)
{
throw new Exception("Input file not a valid file format to parse.");
}
//Finds a formatter and opens the file
ISequenceFormatter outputFormatter = SequenceFormatters.FindFormatterByFileName(this.OutputFile);
if (outputFormatter == null)
{
throw new Exception("Output file not a valid file format for conversion.");
}
try
{
foreach (ISequence sequence in inputParser.Parse())
{
outputFormatter.Format(sequence);
}
}
catch
{
throw new OperationCanceledException(
string.Format(
"Unable to convert sequences from {0} to {1} - verify that the input sequences have the appropriate type of data to convert to the output formatter.",
inputParser.Name,
outputFormatter.Name));
}
finally
{
outputFormatter.Close();
inputParser.Close();
}
}
private void save_Click(object sender, RoutedEventArgs e)
{
if (changeTextBox.Text != null)
{
InitializeSaveSequenceFileDialog();
if (saveEditSequenceFileDialog.ShowDialog() == true)
{
try
{
string sequenceToSave = changeTextBox.Text;
ISequence seq = new Bio.Sequence(Alphabets.DNA, sequenceToSave);
ISequenceFormatter formatter = SequenceFormatters.FindFormatterByFileName(saveEditSequenceFileDialog.FileName);
formatter.Write(seq);
formatter.Close();
}
catch (Exception ex)
{
MessageBoxResult result = ModernDialog.ShowMessage(ex.Message, "Exception", MessageBoxButton.OK);
}
}
}
}
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);
}
}
}
public static void ConvertFromOneFormatToAnother(string inputFileName, string outputFileName, ISequenceFormatter targetFormatter)
{
var parser = SequenceParsers.FindParserByFileName(inputFileName);
var sequenceList = parser.Parse();
var sequences = Helper.ConvertIenumerableToList(sequenceList);
targetFormatter.Open(outputFileName);
foreach (var sequence in sequences)
{
targetFormatter.Write(sequence);
}
targetFormatter.Close();
targetFormatter.Dispose();
}
