public ActionResult GetBlastSearchResult(string projectId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
return(Json(bioService.GetBlastSearchResult(project, Server.MapPath("~/ServiceResults/"), GetActualUserProject())));
}
private IList <AlignRecord> GetRecordsFromResult(ObjectId projectId, IList <string> records)
{
IList <AlignRecord> alignRecords = new List <AlignRecord>();
SequenceProject sProject = db.GetItem <SequenceProject>(x => x._id == projectId);
if (sProject != null)
{
IList <Sequence> sequences = GetSequenceForProject(projectId.ToString(), null);
int index = 0;
while (index < records.Count)
{
if (records[index].StartsWith(">"))
{
AlignRecord record = new AlignRecord();
record.AlignedSequence = records[index + 1];
record.SequenceHeader = records[index];
Sequence findedSeq = sequences.FirstOrDefault(x => x.FastaProtein.StartsWith(records[index]));
index += 2;
if (findedSeq != null)
{
record.SequenceId = findedSeq._id;
record.SequenceName = findedSeq.Name;
record.Organism = findedSeq.Organism;
alignRecords.Add(record);
}
}
}
}
return(alignRecords);
}
public DataSourceResult GetAlignmentForProject([DataSourceRequest] DataSourceRequest request, string projectId)
{
foreach (Kendo.Mvc.SortDescriptor sd in request.Sorts)
{
sd.Member = ConvertSequenceViewModel(sd.Member);
}
foreach (Kendo.Mvc.FilterDescriptor fd in request.Filters.Where(x => x is Kendo.Mvc.FilterDescriptor))
{
fd.Member = ConvertSequenceViewModel(fd.Member);
}
foreach (
Kendo.Mvc.CompositeFilterDescriptor fd in request.Filters.Where(x => x is Kendo.Mvc.CompositeFilterDescriptor))
{
ConvertSequenceFilters(fd);
}
ObjectId id = ObjectId.Empty;
if (ObjectId.TryParse(projectId, out id))
{
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == id);
IQueryable <AlignmentSequence> querySeq = project != null && project.Alligments != null?project.Alligments.AsQueryable() : new List <AlignmentSequence>().AsQueryable();
return(querySeq.ToDataSourceResult(request));
}
return(new DataSourceResult());
}
public ActionResult AddTreePicture(FormCollection col, TreeModel model)
{
if (Request.Files.Count > 0)
{
var file = Request.Files[0];
if (file != null && file.ContentLength > 0)
{
string fileName = Path.GetFileName(file.FileName);
var path = Path.Combine(Server.MapPath("~/ServiceResults/Trees/"), fileName);
file.SaveAs(path);
ObjectId projId = ObjectId.Parse(model.ProjectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && model.AlignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == model.AlignmentId);
if (alignment != null)
{
alignment.TreePicture = path;
db.UpdateItem(project);
}
}
}
}
return(RedirectToAction("ViewTree", new { projectId = model.ProjectId, alignmentId = model.AlignmentId }));
}
public ActionResult ViewTree(string projectId, string alignmentId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && alignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == alignmentId);
if (alignment != null && !String.IsNullOrEmpty(alignment.PhylogeneticTree))
{
string fileContent = String.Empty;
if (System.IO.File.Exists(alignment.TreePicture))
{
using (StreamReader sr = new StreamReader(alignment.TreePicture))
{
fileContent = sr.ReadToEnd();
}
}
return(View("ViewTree", new TreeModel()
{
TreeString = alignment.PhylogeneticTree, AlignmentName = alignment.Description, ProjectId = projectId, AlignmentId = alignmentId, TreeFile = fileContent
}));
}
}
return(View());
}
public ActionResult GetTreeResult(string projectId, string alignmentId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
return(Json(bioService.GetSimplePhyloResult(project, alignmentId)));
}
public void SaveProject(SequenceProject project, ObjectId creatorId)
{
if (project._id == ObjectId.Empty)
{
db.AddItem(project, creatorId);
}
else
{
db.UpdateItem(project);
}
}
public DataSourceResult GetSequenceForProject([DataSourceRequest] DataSourceRequest request, string projectId, string[] taxons, bool isBlast = false)
{
foreach (Kendo.Mvc.SortDescriptor sd in request.Sorts)
{
sd.Member = ConvertSequenceViewModel(sd.Member);
}
foreach (Kendo.Mvc.FilterDescriptor fd in request.Filters.Where(x => x is Kendo.Mvc.FilterDescriptor))
{
fd.Member = ConvertSequenceViewModel(fd.Member);
}
foreach (
Kendo.Mvc.CompositeFilterDescriptor fd in request.Filters.Where(x => x is Kendo.Mvc.CompositeFilterDescriptor))
{
ConvertSequenceFilters(fd);
}
ObjectId id = ObjectId.Empty;
if (ObjectId.TryParse(projectId, out id))
{
IQueryable <Sequence> querySeq = null;
if (taxons != null)
{
querySeq = db.GetCollection <Sequence>(x => x.ProjectId == id && x.Lineage != null).AsQueryable();
IList <Sequence> sequences = querySeq.ToList();
IList <Sequence> hlpSequences = new List <Sequence>();
foreach (string taxon in taxons)
{
hlpSequences.AddRange(sequences.Where(x => x.Lineage.Contains(taxon)).ToList());
}
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == id);
project.ActualTaxons = taxons.ToList();
db.UpdateItem(project);
querySeq = hlpSequences.AsQueryable();
}
else
{
querySeq = db.GetCollection <Sequence>(x => x.ProjectId == id).AsQueryable();
}
if (isBlast)
{
querySeq = querySeq.Where(x => !String.IsNullOrEmpty(x.BlastAlignedSequence)).ToList().AsQueryable();
}
else
{
querySeq = querySeq.Where(x => String.IsNullOrEmpty(x.BlastAlignedSequence)).ToList().AsQueryable();
}
return(querySeq.ToDataSourceResult(request));
}
return(new DataSourceResult());
}
public void GenerateBlastSearch(ObjectId projectId, Models.BlastModels.BlastViewModel model)
{
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projectId);
if (project != null)
{
blastService.SetParams(new ServiceConnector.BlastConnector.InputParameters()
{
stype = "protein", program = "blastp", matrix = "BLOSUM62", sequence = model.Sequence, database = new string[] { model.DatabaseParam }, scores = Int32.Parse(model.ScoresParam)
});
project.BlastSearchGuid = blastService.Run("BlastSearch");
db.UpdateItem(project);
}
}
public bool SelUnSelAllSequence(string projectId, bool sel, bool isBlast)
{
ObjectId id = ObjectId.Empty;
if (ObjectId.TryParse(projectId, out id))
{
var querySeq = isBlast ? db.GetCollection <Sequence>(x => x.ProjectId == id && !String.IsNullOrEmpty(x.BlastAlignedSequence)).ToList() :
db.GetCollection <Sequence>(x => x.ProjectId == id && String.IsNullOrEmpty(x.BlastAlignedSequence)).ToList();
querySeq.ForEach(x => x.Selected = sel);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == id);
project.ActualTaxons = new List <string>();
db.UpdateItem(project);
UpdateSequenceData(querySeq);
}
return(false);
}
public ActionResult ViewAlignment(string projectId, string alignmentId)
{
ObjectId projId = ObjectId.Parse(projectId);
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projId);
if (project != null && alignmentId != String.Empty)
{
AlignmentSequence alignment = project.Alligments.First(x => x.IdString == alignmentId);
if (alignment != null && alignment.AllignedSequences != null && alignment.AllignedSequences.Any())
{
return(View("ViewAlignmentRaw", new AlignmentModel()
{
AlignmentSequences = alignment.AllignedSequences, AlignmentName = alignment.Description, AlignmentId = alignmentId, ProjectId = projectId
}));
}
}
return(View(new HtmlString("")));
}
public bool GetSimplePhyloResult(SequenceProject project, string alignmentId)
{
IList <string> records = new List <string>();
if (project != null && project.Alligments != null)
{
AlignmentSequence alignment = project.Alligments.First(x => x._id == ObjectId.Parse(alignmentId));
string result = alignment.PhylogeneticFilename + ".tree.ph";
if (alignment != null)
{
if (!File.Exists(result))
{
result = phylologyService.GetResults(alignment.PhylogeneticGuid, alignment.PhylogeneticFilename);
if (String.IsNullOrEmpty(result))
{
return(false);
}
result = result + ".tree.ph";
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
while (!sr.EndOfStream)
{
string hlpString = sr.ReadLine();
sb.AppendLine(hlpString);
records.Add(hlpString);
}
foreach (string s in records)
{
alignment.PhylogeneticTree += s;
}
db.UpdateItem(project);
return(true);
}
}
}
}
return(false);
}
public bool GetClustalResult(SequenceProject project, string alignmentId)
{
IList <string> records = new List <string>();
if (project != null && project.Alligments != null)
{
AlignmentSequence alignment = project.Alligments.First(x => x._id == ObjectId.Parse(alignmentId));
string result = alignment.AlignmentFilename + ".vienna.aln-vienna.vienna";
if (alignment != null)
{
if (!File.Exists(result))
{
result = clustalService.GetResults(alignment.AlignmentGuid, alignment.AlignmentFilename);
if (String.IsNullOrEmpty(result))
{
return(false);
}
result = result + ".aln-vienna.vienna";
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
while (!sr.EndOfStream)
{
string hlpString = sr.ReadLine();
sb.AppendLine(hlpString);
records.Add(hlpString);
}
alignment.AllignedSequences = GetRecordsFromResult(project._id, records);
alignment.IsFinished = true;
db.UpdateItem(project);
return(true);
}
}
}
}
return(false);
}
private IList <Sequence> CreateBlastSequencies(hits hits, SequenceProject project, UserProject userProject)
{
IList <Sequence> sequencies = new List <Sequence>();
if (hits != null && hits.seqHits != null)
{
WebClient webClient = new WebClient();
foreach (hit hit in hits.seqHits)
{
if (IsReadyForUpdate(hit.alignmets))
{
Sequence sequence = new Sequence();
sequence.ProjectId = userProject.ProjectId;
//výsledek zarovnání blast
sequence.BlastAlignedSequence = hit.alignmets.alignment[0].patternSeq.matchSeqValue;
//fasta organismu
sequence.FastaProtein = hit.alignmets.alignment[0].matchSeq.matchSeqValue;
sequence.Created = DateTime.Now;
sequence.Description = hit.description;
PopulateLineageBlast(sequence, webClient);
if (!String.IsNullOrEmpty(sequence.Organism) && sequence.Lineage != null && sequence.Lineage.Any())
{
if (!sequence.Name.Contains("Fragment"))
{
if (!sequencies.Select(x => x.Organism).Contains(sequence.Organism))
{
sequencies.Add(sequence);
}
}
}
}
}
db.AddItems(sequencies, userProject.UserId);
}
return(sequencies);
}
public void GenerateTree(ObjectId projectId, string alignmentId, string path)
{
SequenceProject project = db.GetItem <SequenceProject>(x => x._id == projectId);
if (project != null)
{
AlignmentSequence aligment = project.Alligments.FirstOrDefault(x => x.IdString == alignmentId);
if (aligment != null)
{
string seq = String.Empty;
foreach (AlignRecord rec in aligment.AllignedSequences)
{
seq += ">" + rec.Organism.Replace(" ", "_") + "\n" + rec.AlignedSequence + "\n";
}
phylologyService.SetParams(new ServiceConnector.PhylogenyConnector.InputParameters()
{
sequence = seq, tree = "phylip"
});
aligment.PhylogeneticGuid = phylologyService.Run(aligment.Description);
aligment.PhylogeneticFilename = path + aligment.PhylogeneticGuid;
db.UpdateItem(project);
}
}
}
public bool GetBlastSearchResult(SequenceProject project, string path, UserProject userProject)
{
if (project != null)
{
//XmlResult
string result = path + project.BlastSearchGuid + ".xml.xml";
if (!File.Exists(result))
{
result = blastService.GetResults(project.BlastSearchGuid, result);
if (String.IsNullOrEmpty(result))
{
return(false);
}
}
if (!String.IsNullOrEmpty(result))
{
using (StreamReader sr = new StreamReader(result))
{
StringBuilder sb = new StringBuilder();
XmlReader reader = XmlReader.Create(sr);
EBIApplicationResult ebiResult = GenerateSequencesFromXml(reader);
if (ebiResult != null && ebiResult.SequenceSimilaritySearchResult != null)
{
IList <Sequence> sequencies = CreateBlastSequencies(ebiResult.SequenceSimilaritySearchResult.hits, project, userProject);
if (project.Alligments == null)
{
project.Alligments = new List <AlignmentSequence>();
}
if (sequencies != null && sequencies.Any())
{
AlignmentSequence allign = new AlignmentSequence()
{
Created = DateTime.Now,
CreatorId = project.CreatorId,
Description = "BlastAlignment",
IsFinished = false,
_id = ObjectId.GenerateNewId(),
Source = "Blast",
AllignedSequences = new List <AlignRecord>()
};
foreach (Sequence seq in sequencies)
{
allign.AllignedSequences.Add(new AlignRecord()
{
AlignedSequence = seq.BlastAlignedSequence,
Organism = seq.Organism,
SequenceId = seq._id,
SequenceName = seq.Name,
SequenceHeader = seq.Description
});
}
project.Alligments.Add(allign);
db.UpdateItem(project);
return(true);
}
}
}
}
}
return(false);
}
