/// <summary>
/// Fetch results asynchronous
/// </summary>
/// <param name="blastParameters">Blast Input config parameters</param>
/// <returns></returns>
private TestCaseOutput FetchResultsAsync(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
Sequence sequence = new Sequence(Alphabets.DNA, sequenceString);
// Set NCBIHandler configuration services
IBlastServiceHandler service = null;
object resultsObject = null;
try
{
service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Get Request identifier from web service.
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// Get request information for first time.
ServiceRequestInformation info = service.GetRequestStatus(reqId);
// Ping service until request staus is ready.
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts && info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Error)
{
System.Threading.Thread.Sleep(2000);
++attempt;
info = service.GetRequestStatus(reqId);
}
IBlastParser blastXmlParser = new BlastXmlParser();
using (StringReader reader = new StringReader(service.GetResult(reqId, blastSearchPams)))
{
resultsObject = blastXmlParser.Parse(reader);
}
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(resultsObject, false));
}
/// <summary>
/// Validate a Azure Blast Service constructor with invalid parameters.
/// Input : Invalid service config parameters.
/// Output : Invalidate Azure web service constructor.
/// </summary>
public void InvalidateAzureWebHandlerCtor()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 10;
configParams.Connection = new Uri(Constants.AzureUri);
BlastXmlParser parser = new BlastXmlParser();
// Validate AzureWebService ctor by passing null parser.
IBlastServiceHandler service = null;
try
{
service = new AzureBlastHandler(null, configParams);
Assert.IsNotNull(service);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
// Validate AzureWebService ctor by passing null configuration parameters.
try
{
service = new AzureBlastHandler(parser, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// When implemented in a derived class and using the specified execution environment information, notifies the workflow runtime that the associated asynchronous activity operation has completed.
/// </summary>
/// <returns>
/// A generic type.
/// </returns>
/// <param name="context">Information that defines the execution environment for the <see cref="T:System.Activities.AsyncCodeActivity"/>.</param>
/// <param name="asyncResult">The implemented <see cref="T:System.IAsyncResult"/> that returns the status of an asynchronous activity when execution ends.</param>
protected override string EndExecute(AsyncCodeActivityContext context, IAsyncResult asyncResult)
{
var runningTask = context.UserState as Task <Stream>;
// Get blast result.
BlastXmlParser blastParser = new BlastXmlParser();
IList <BlastResult> results = blastParser.Parse(runningTask.Result).ToList();
// Convert blast result to BlastCollator.
List <BlastResultCollator> blastResultCollator = new List <BlastResultCollator>();
foreach (BlastResult result in results)
{
foreach (BlastSearchRecord record in result.Records)
{
if (record.Hits != null && 0 < record.Hits.Count)
{
foreach (Hit hit in record.Hits.Where(hit => hit.Hsps != null && 0 < hit.Hsps.Count))
{
blastResultCollator.AddRange(hit.Hsps.Select(hsp =>
new BlastResultCollator
{
Alignment = hsp.AlignmentLength,
Bit = hsp.BitScore,
EValue = hsp.EValue,
Identity = hsp.IdentitiesCount,
Length = hit.Length,
QEnd = hsp.QueryEnd,
QStart = hsp.QueryStart,
QueryId = record.IterationQueryId,
SEnd = hsp.HitEnd,
SStart = hsp.HitStart,
SubjectId = hit.Id,
Positives = hsp.PositivesCount,
QueryString = hsp.QuerySequence,
SubjectString = hsp.HitSequence,
Accession = hit.Accession,
Description = hit.Def
}));
}
}
}
}
BlastXmlSerializer serializer = new BlastXmlSerializer();
Stream stream = serializer.SerializeBlastOutput(blastResultCollator);
// set result to the output property.
return(GetSerializedData(stream));
}
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 async Task <string> SearchBlast(string seqString, CancellationToken cancellationToken)
{
NcbiBlastWebHandler handler = new NcbiBlastWebHandler()
{
LogOutput = Log,
EndPoint = "https://www.ncbi.nlm.nih.gov/blast/Blast.cgi",
TimeoutInSeconds = 3600
};
string cleanDNASequence = new string(seqString.Where(c => c == 'A' || c == 'G' || c == 'T' || c == 'C').ToArray());
Sequence sequence = new Sequence(DnaAlphabet.Instance, cleanDNASequence);
List <Bio.ISequence> sequences = new List <Bio.ISequence>();
sequences.Append(sequence);
var request = new BlastRequestParameters(sequences)
{
Database = "nt",
Program = BlastProgram.Blastn
};
request.Sequences.Add(sequence);
HttpContent result = handler.BuildRequest(request);
var executeResult = await handler.ExecuteAsync(request, cancellationToken);
if (executeResult == null)
{
return("Your sequence is not found (hits=0)");
}
//Stream stream = await result.ReadAsStreamAsync();
Bio.Web.Blast.BlastXmlParser parser = new BlastXmlParser();
var results = parser.Parse(executeResult).ToList();
var resString = String.Join(Environment.NewLine,
results.FirstOrDefault()
.Records.FirstOrDefault()
.Hits.Take(5)
.Select(x => $"ID: {x.Id}, Accession: {x.Accession}, Def: {x.Def}")
.ToArray());
return(resString);
}
public void InvalidateBioHPCBlastHandler()
{
try
{
IBlastServiceHandler handler = new BioHPCBlastHandler(null, new ConfigParameters());
Assert.Fail();
}
catch (ArgumentNullException anex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentNullException : " + anex.Message);
}
try
{
IBlastParser blastXmlParser = new BlastXmlParser();
IBlastServiceHandler handler = new BioHPCBlastHandler(blastXmlParser, null);
Assert.Fail();
}
catch (ArgumentNullException anex)
{
ApplicationLog.WriteLine("Successfully caught ArgumentNullException : " + anex.Message);
}
}
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;
}
/// <summary>
/// Validates general Add method test cases with the xml node name specified.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="isSyncFetch">True for Synchronous fetch</param>
void GeneralMethodToValidateResults(string nodeName, bool isSyncFetch)
{
// Gets the search query parameter and their values.
string alphabet = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedHspHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HspHitsCount);
string expectedSleepTime = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SleepTime);
string reqId = string.Empty;
object responseResults = null;
int maxAttempts = 20;
int attempt = 1;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
// Create search parameters object.
BlastParameters searchParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
// Get Request identifier from web service.
reqId = service.SubmitRequest(seq, searchParams);
// Get request information for first time.
ServiceRequestInformation info = service.GetRequestStatus(reqId);
// Ping service until request staus is ready.
while (attempt <= maxAttempts && info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Error)
{
System.Threading.Thread.Sleep(Convert.ToInt32(expectedSleepTime, (IFormatProvider)null));
++attempt;
info = service.GetRequestStatus(reqId);
}
// Get results.
if (isSyncFetch)
{
responseResults = service.FetchResultsSync(reqId, searchParams);
}
else
{
responseResults = service.GetResult(reqId, searchParams);
}
Assert.IsNotNull(responseResults);
if (!isSyncFetch)
{
//Parse and validate results
BlastXmlParser parser = new BlastXmlParser();
IList <BlastResult> blastResults =
parser.Parse(new StringReader(responseResults.ToString()));
Assert.AreEqual(blastResults.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Assert.AreEqual(blastResults[0].Records.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
BlastSearchRecord record = blastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null), expectedHspHitsCount);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Accession '{0}'.", hit.Accession));
}
}
/// <summary>
/// Fetch Asynchronous results
/// </summary>
/// <param name="blastParameters">Blast config parameters</param>
/// <returns>BioHPC Web service results</returns>
private TestCaseOutput FetchResultsASyncTest(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
string alphabetName = blastParameters[Constants.AlphabetString] as string;
string email = blastParameters[Constants.EmailString] as string;
Sequence sequence = new Sequence(Utility.GetAlphabet(alphabetName),
sequenceString);
string maxAttempts = blastParameters[Constants.MaxAttemptString] as string;
string waitTime = blastParameters[Constants.WaitTimeString] as string;
//Set BioHPC web service config parameters
IBlastServiceHandler service = null;
object responseResults = null;
try
{
service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Submit request and get request identifier
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// validate request identifier.
Assert.IsNotNull(reqId);
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Queued)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'",
info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int attempt = 1;
while (attempt <= Int32.Parse(maxAttempts, (IFormatProvider)null) &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
++attempt;
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? Int32.Parse(waitTime, (IFormatProvider)null) * attempt : 0);
}
IBlastParser blastXmlParser = new BlastXmlParser();
using (StringReader reader = new StringReader(service.GetResult(reqId, blastSearchPams)))
{
responseResults = blastXmlParser.Parse(reader);
}
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(responseResults, false));
}
/// <summary>
/// The execution method for the activity.
/// </summary>
/// <param name="executionContext">The execution context.</param>
/// <returns>The execution status.</returns>
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
FastAParser fastaParser = new FastAParser();
fastaParser.Open(InputFile);
ISequence searchSequence = fastaParser.Parse().FirstOrDefault();
NCBIBlastHandler service = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// fill in the BLAST settings:
searchParams.Add("Program", "blastn");
searchParams.Add("Database", "nr");
// higher Expect will return more results
searchParams.Add("Expect", "1e-10");
searchParams.Add("CompositionBasedStatistics", "0");
// create the request
string jobID = service.SubmitRequest(searchSequence, searchParams);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(jobID);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
// TODO: Add error handling here
}
// get async results, poll until ready
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
++attempt;
info = service.GetRequestStatus(jobID);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting || info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
}
// Get blast result.
BlastXmlParser blastParser = new BlastXmlParser();
IList <BlastResult> results = blastParser.Parse(new StringReader(service.GetResult(jobID, searchParams)));
// Convert blast result to BlastCollator.
List <BlastResultCollator> blastResultCollator = new List <BlastResultCollator>();
foreach (BlastResult result in results)
{
foreach (BlastSearchRecord record in result.Records)
{
if (null != record.Hits &&
0 < record.Hits.Count)
{
foreach (Hit hit in record.Hits)
{
if (null != hit.Hsps &&
0 < hit.Hsps.Count)
{
foreach (Hsp hsp in hit.Hsps)
{
BlastResultCollator blast = new BlastResultCollator();
blast.Alignment = hsp.AlignmentLength;
blast.Bit = hsp.BitScore;
blast.EValue = hsp.EValue;
blast.Identity = hsp.IdentitiesCount;
blast.Length = hit.Length;
blast.QEnd = hsp.QueryEnd;
blast.QStart = hsp.QueryStart;
blast.QueryId = record.IterationQueryId;
blast.SEnd = hsp.HitEnd;
blast.SStart = hsp.HitStart;
blast.SubjectId = hit.Id;
blast.Positives = hsp.PositivesCount;
blast.QueryString = hsp.QuerySequence;
blast.SubjectString = hsp.HitSequence;
blast.Accession = hit.Accession;
blast.Description = hit.Def;
blastResultCollator.Add(blast);
}
}
}
}
}
}
BlastXmlSerializer serializer = new BlastXmlSerializer();
Stream stream = serializer.SerializeBlastOutput(blastResultCollator);
// set result to the output property.
BlastResult = GetSerializedData(stream);
return(ActivityExecutionStatus.Closed);
}
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[] 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);
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for Ebi web service..
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateEBIWuBlastResultsFetch(
string nodeName,
bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string emailParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Length);
object responseResults = null;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create Ebi Blast service object.
IBlastServiceHandler service = new EbiWuBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(emailParameter, email);
searchParams.Add("SequenceType",
alphabetName.ToLower(CultureInfo.CurrentCulture).Replace("ambiguous", ""));
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 20;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
}
else
{
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ? 20000 : 0);
info = service.GetRequestStatus(reqId);
}
++attempt;
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List <BlastResult> eBlastResults = responseResults as List <BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString((IFormatProvider)null), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList <BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List <BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != eBlastResults[0].Records[0].Hits &&
0 < eBlastResults[0].Records[0].Hits.Count &&
null != eBlastResults[0].Records[0].Hits[0].Hsps &&
0 < eBlastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(eBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine(
"No significant hits found with the these parameters.");
Console.WriteLine("No significant hits found with the these parameters.");
}
}
}
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 void EBIWuBlastResultsWithQueryParams()
{
// Gets the search query parameter and their values.
string alphabetName = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.DatabaseValue);
string emailParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.Emailparameter);
string email = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.EmailAdress);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramParameter);
string expectedHitId = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitID);
string expectedAccession = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitAccession);
string expectedResultCount = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ResultsCount);
string expectedHitsCount = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitsCount);
string expectedEntropyStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.EntropyStatistics);
string expectedKappaStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.KappaStatistics);
string expectedLambdaStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.LambdaStatistics);
string expectedLength = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.Length);
object responseResults = null;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create Ebi Blast service object.
IBlastServiceHandler service = new EbiWuBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(emailParameter, email);
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err = ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 15;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting ? 20000 : 0);
info = service.GetRequestStatus(reqId);
++attempt;
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List <BlastResult> eBlastResults = responseResults as List <BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString(), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null), expectedResultCount);
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits Length '{0}'.", hit.Length));
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for BioHPC Blast web service.
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
static void ValidateBioHPCBlastResultsFetch(
string nodeName,
bool isFetchSynchronous)
{
if (_IsWebServiceAvailable)
{
// Gets the search query parameter and their values.
string alphabetName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
nodeName,
Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics =
Utility._xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = Utility._xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = Utility._xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Length);
int maxAttempts = int.Parse(Utility._xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode));
int waitingTime = int.Parse(Utility._xmlUtil.GetTextValue(
nodeName, Constants.WaitingTimeNode));
string expect = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
object responseResults = null;
Sequence seq = new Sequence(
Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configPams = new ConfigParameters();
configPams.EmailAddress = email;
configPams.Password = String.Empty;
configPams.UseBrowserProxy = true;
service.Configuration = configPams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Queued)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'",
info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
++attempt;
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? waitingTime * attempt : 0);
}
else
{
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued ?
waitingTime * attempt : 0);
info = service.GetRequestStatus(reqId);
}
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List <BlastResult> eBlastResults =
responseResults as List <BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString(), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null),
expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Hits Count '{0}'.", hit.Hsps.Count));
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList <BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List <BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != eBlastResults[0].Records[0].Hits &&
0 < eBlastResults[0].Records[0].Hits.Count &&
null != eBlastResults[0].Records[0].Hits[0].Hsps &&
0 < eBlastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(
eBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine(
"No significant hits found with the these parameters.");
Console.WriteLine(
"No significant hits found with the these parameters.");
}
}
}
else
{
Assert.Ignore(
"The test case ignored due to connection failure");
}
}
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);
}
}
}
/// <summary>
/// Validate Fetch results synchronous.
/// </summary>
/// <param name="blastParameters">Ebi blast service config parameters</param>
/// <returns></returns>
private TestCaseOutput FetchResultsASync(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
string alphabetName = blastParameters[Constants.AlphabetString] as string;
Sequence sequence = new Sequence(Utility.GetAlphabet(alphabetName),
sequenceString);
// create Ebi Blast service object.
object responseResults = null;
IBlastServiceHandler service = null;
try
{
service = new EbiWuBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Create a request without passing sequence.
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// validate request identifier.
Assert.IsNotNull(reqId);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 3;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
++attempt;
}
IBlastParser blastXmlParser = new BlastXmlParser();
using (StringReader reader = new StringReader(service.GetResult(reqId, blastSearchPams)))
{
responseResults = blastXmlParser.Parse(reader);
}
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(responseResults, false));
}
private void DoBLAST(string filename)
{
// Update progress bar, set content of user control to initial state
// Load protein sequences
FastaParser parser = new FastaParser();
IList<ISequence> queryList = parser.Parse(filename).ToList();
// Initialize and populate queue of query sequences
Queue<QueueSequence> queryQueue = new Queue<QueueSequence>();
int j = 0; // For debuging
int progValue = 0;
int currentProgress = 0;
foreach (ISequence protein in queryList)
{
QueueSequence qp = new QueueSequence();
qp.Sequence = protein;
qp.Position = j;
string name = j.ToString();
j++;
if (File.Exists(Up.ProjectDir + "\\xml\\" + name + ".xml"))
{
IList<BlastResult> blastResults;
BlastXmlParser parser2 = new BlastXmlParser();
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
progValue = Convert.ToInt32(Math.Round((double)currentProgress / queryList.Count() * 100, 0));
UpdateProgressBar(progValue, "Validating BLAST results.");
currentProgress++;
}
catch
{
queryQueue.Enqueue(qp);
}
}
else
{
queryQueue.Enqueue(qp);
}
}
// Initialize BLAST queue positions to having no jobs (EMPTY)
BlastQueue blastQueue = new BlastQueue();
// While there are proteins left to submit to BLAST, or there are
// busy jobs still on the queue
UpdateProgressBar(progValue, "Starting up BLAST service, please wait.");
while (queryQueue.Count > 0 || blastQueue.isBlastQueueBusy())
{
// Iterate over blastQueue
for (int i = 0; i < BlastQueue.Length; i++)
{
// Get blastJob from array and update status
BlastJob blastJob = blastQueue[i];
QueueSequence qp = new QueueSequence();
qp.Sequence = blastJob.Query;
qp.Position = blastJob.Position;
// if queue position is AVAILABLE
if (blastJob.JobStatus == BlastJob.AVAILABLE)
{
if (queryQueue.Count > 0)
{
QueueSequence qp2 = queryQueue.Dequeue();
// try to submit job, enqueue back the protein if submission failed.
try
{
blastQueue[i] = submit(qp2);
if (blastQueue[i].JobStatus == BlastJob.FAILED)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp2);
}
else
{
UpdateProgressBar(progValue, "Submitting sequences to NCBI BLAST");
}
}
catch (Exception eee)
{
MessageBox.Show(eee.Message);
}
}
}
else
{
string jobId = blastJob.JobId;
NCBIBlastHandler blastService = blastJob.BlastService;
ServiceRequestInformation info = blastService.GetRequestStatus(jobId);
Thread.Sleep(BlastQueue.RequestDelay);
switch (info.Status)
{
case ServiceRequestStatus.Error:
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
break;
case ServiceRequestStatus.Canceled:
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
break;
case ServiceRequestStatus.Ready:
string result = blastService.GetResult(jobId, blastJob.SearchParams);
string name = blastJob.Position.ToString();
TextWriter tw = new StreamWriter(Up.ProjectDir + "\\xml\\" + name + ".xml");
tw.Write(result);
tw.Close();
Debug.WriteLine("BLAST JOB: " + jobId + " , " + name + " , " + info.StatusInformation);
// Added by VF on Jan, 22, 2013. Catches invalid BLAST records
IList<BlastResult> blastResults;
BlastXmlParser parser2 = new BlastXmlParser();
bool parsePassed = false;
int fetchAttempts = 0;
while (!parsePassed && fetchAttempts < 3)
{
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
parsePassed = true;
Debug.WriteLine("FETCH OK JobId: " + jobId + " InputOrder: " + name + ". This is attempt:" + fetchAttempts.ToString());
}
catch (Exception eee)
{
Debug.WriteLine("Trying to fetch JobId: " + jobId + " InputOrder: " + name + ". This is attempt: " + fetchAttempts.ToString());
parsePassed = false;
result = blastService.GetResult(jobId, blastJob.SearchParams);
TextWriter tw2 = new StreamWriter(Up.ProjectDir + "\\xml\\" + name + ".xml");
tw2.Write(result);
tw2.Close();
fetchAttempts += 1;
}
Thread.Sleep(1000);
}
try
{
blastResults = parser2.Parse(Up.ProjectDir + "\\xml\\" + name + ".xml");
}
catch (Exception eee)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp);
Debug.WriteLine("REQUEUE of JobId: " + " " + jobId + " InputOrder: " + name + " because max fetch is " + fetchAttempts.ToString());
break;
}
currentProgress += 1;
progValue = Convert.ToInt32(Math.Round((double)currentProgress / queryList.Count() * 100, 0));
UpdateProgressBar(progValue, "Saving");
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
if (queryQueue.Count > 0)
{
QueueSequence qp3 = queryQueue.Dequeue();
try
{
blastQueue[i] = submit(qp3);
if (blastQueue[i].JobStatus == BlastJob.FAILED)
{
blastQueue[i].JobStatus = BlastJob.AVAILABLE;
queryQueue.Enqueue(qp3);
}
else
{
UpdateProgressBar(progValue, "Submitting sequences to NCBI BLAST");
}
}
catch (Exception eee)
{
MessageBox.Show(eee.Message);
MessageBox.Show("Error creating a jobId for sequence " + qp3.Position);
throw new Exception("Error creating a jobId for sequence" + qp3.Position);
}
}
break;
case ServiceRequestStatus.Queued:
break;
case ServiceRequestStatus.Waiting:
break;
default:
MessageBox.Show("BLAST error " + info.Status + " " + blastJob.JobStatus + " for " + qp.Position);
break;
}
}
}
}
}
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");
}
}
