public void FastaParserForManyFiles()
{
string path = @"TestUtils\FASTA";
Assert.IsTrue(Directory.Exists(path));
int count = 0;
FastaParser parser = new FastaParser();
FastaFormatter formatter = new FastaFormatter();
DirectoryInfo di = new DirectoryInfo(path);
foreach (FileInfo fi in di.GetFiles("*.fasta"))
{
using (StreamReader reader = File.OpenText(fi.FullName))
{
ApplicationLog.WriteLine("parsing file {0}...", fi.FullName);
foreach (Sequence seq in parser.Parse(reader))
{
ApplicationLog.Write(formatter.FormatString(seq));
count++;
}
}
ApplicationLog.WriteLine("parsing file {0}...", fi.FullName);
}
Assert.IsTrue(count >= 3);
((FastaParser)parser).Dispose();
}
/// <summary>
/// Get the blast service request object with all the request parameter set
/// </summary>
/// <param name="sequence">Input sequece</param>
/// <param name="parameters">Blast parameters</param>
/// <returns>Blast service request object</returns>
private static BlastSerivceRequest GetRequestParameter(
ISequence sequence,
BlastParameters parameters)
{
BlastSerivceRequest blastParameter = new BlastSerivceRequest();
// Sets the format of output expected from Azure Blast service
blastParameter.OptionM = OPTIONMVALUE;
// Sets the name of Job owner
blastParameter.Owner = Resources.OWNERVALUE;
blastParameter.ParitionNumber = PARTITIONVALUE;
// Convert string to byte
ISequenceFormatter formatter = new FastaFormatter();
string inputContent = formatter.FormatString(sequence);
ASCIIEncoding asciiEncoding = new ASCIIEncoding();
blastParameter.InputContent = asciiEncoding.GetBytes(inputContent);
// Other parameters
// Set the Title of Job
blastParameter.Title = sequence.ID;
// Name of the database to be searched in
blastParameter.DatabaseName = parameters.Settings[PARAMETERDATABASE];
// Type of search program to be executed
blastParameter.ProgramName = parameters.Settings[PARAMETERPROGRAM];
return(blastParameter);
}
private void WriteAlignment(SequenceAlignment alignment)
{
FastaFormatter formatter = new FastaFormatter();
StreamWriter alnoutput = new StreamWriter(_tempDirectory + CRWSequenceAlignmentFormatTags.AlignmentFileName);
alnoutput.AutoFlush = true;
foreach (ISequence sequence in alignment.Sequences)
{
alnoutput.Write(formatter.FormatString(sequence));
}
alnoutput.Close();
}
/// <summary>
/// CreateJob() to get job id and control id and Submit job
/// using input sequence with job id and control id
/// </summary>
/// <param name="sequence">input sequences</param>
/// <param name="parameters">input params</param>
/// <returns>result params with job id and control id</returns>
public ServiceParameters SubmitRequest(IList <ISequence> sequence, ClustalWParameters parameters)
{
ServiceParameters result = new ServiceParameters();
// ClusterOption = biosim cbsum1 cbsum2k8 cbsusrv05 cbsum2 or Auto
string[] output = _baseClient.CreateJob(tAppId.P_CLUSTALW, "test_BioHPC_Job", "1", parameters.Values[ClustalWParameters.Email].ToString(),
string.Empty, parameters.Values[ClustalWParameters.ClusterOption].ToString());
if (!output[0].Contains(ERROR))
{
result.JobId = output[1];
result.Parameters.Add(CONTROLID, output[2]);
AppInputData inputData = _baseClient.InitializeApplicationParams(tAppId.P_CLUSTALW, "test_BioHPC_Job");
FastaFormatter formatter = new FastaFormatter();
StringBuilder inputSequence = new StringBuilder();
foreach (ISequence seq in sequence)
{
inputSequence.AppendLine(formatter.FormatString(seq));
}
//formatter.Format(sequence, "temp");
//StreamReader reader = new StreamReader("temp");
inputData.clustalw.inputsource = QuerySrcType.paste;
inputData.clustalw.inputstring = inputSequence.ToString();
inputData.clustalw.isDNA = false;
inputData.clustalw.action = (ClwActions)Enum.Parse(typeof(ClwActions),
parameters.Values[ClustalWParameters.ActionAlign].ToString());
inputData.clustalw.email_notify = true;
_baseClient.SubmitJob(result.JobId, result.Parameters[CONTROLID].ToString(), inputData);
result.Parameters.Add(SUBMISSONRESULT, SUCCESS);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
// Start the BackGroundThread to check the status of job
_workerThread = new BackgroundWorker();
_workerThread.WorkerSupportsCancellation = true;
_workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
_workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
_workerThread.RunWorkerAsync(result);
}
}
else
{
result.Parameters.Add(SUBMISSONRESULT, output[0]);
}
return(result);
}
public void FastaFormatterWithParseValidateFormatString()
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastaNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: File Exists in the Path '{0}'.", filePath));
FastaParser parser = new FastaParser();
FastaFormatter formatter = new FastaFormatter();
// Read the original file
IList <ISequence> seqsOriginal = null;
parser = new FastaParser();
seqsOriginal = parser.Parse(filePath);
Assert.IsNotNull(seqsOriginal);
string formatStrOrginal = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastaNodeName,
Constants.FormatStringNode);
string formatStr = formatter.FormatString(seqsOriginal[0]).Trim();
formatStr = formatStr.Replace("\r", "").Replace("\n", "");
Assert.AreEqual(formatStrOrginal, formatStr);
Console.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with FormatString() method and is as expected.",
formatStrOrginal));
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with FormatString() method.",
formatStrOrginal));
}
public void FastaFormatterValidateFormatString()
{
FastaFormatter formatter = new FastaFormatter();
// Gets the actual sequence and the alphabet from the Xml
string actualSequence = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
string alpName = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: Validating with Sequence '{0}' and Alphabet '{1}'.",
actualSequence, alpName));
Sequence seqOriginal = new Sequence(Utility.GetAlphabet(alpName),
actualSequence);
Assert.IsNotNull(seqOriginal);
seqOriginal.ID = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.SequenceIdNode);
string formatStrOrginal = Utility._xmlUtil.GetTextValue(
Constants.SimpleFastaNodeName, Constants.FormatStringNode);
string formatStr = formatter.FormatString(seqOriginal);
formatStr = formatStr.Replace("\r", "").Replace("\n", "");
Assert.AreEqual(formatStrOrginal, formatStr);
Console.WriteLine(
string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with FormatString() method and is as expected.",
formatStrOrginal));
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with FormatString() method.",
formatStrOrginal));
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the MBF.IO formatters
/// to convert the sequence into the web interface compliant sequence format.
/// This method performs parameter validation and throw Exception on invalid input.
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequence">The sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(ISequence sequence, BlastParameters parameters)
{
if (null == sequence)
{
throw new ArgumentNullException("sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
if (!string.IsNullOrEmpty(Configuration.EmailAddress))
{
if (!parameters.Settings.ContainsKey(ParameterEmail))
{
parameters.Add(ParameterEmail, Configuration.EmailAddress);
}
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
inputParams blastRequest = GetRequestParameter(parameters);
blastRequest.appxml = AppXmlYes;
blastRequest.async = true;
data[] mydata = new data[1];
mydata[0] = new data();
mydata[0].type = SequenceType;
FastaFormatter formatter = new FastaFormatter();
mydata[0].content = formatter.FormatString(sequence);
requestIdentifier = _blastClient.runWUBlast(blastRequest, mydata);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
ThreadParameter threadParameter = new ThreadParameter(
requestIdentifier,
sequence,
parameters);
// Start the BackGroundThread to check the status of job
_workerThread = new BackgroundWorker();
_workerThread.WorkerSupportsCancellation = true;
_workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
_workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
_workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the MBF.IO formatters
/// to convert the sequence into the web interface compliant sequence format.
/// This method performs parameter validation and throw Exception on invalid input.
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequence">The sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(ISequence sequence, BlastParameters parameters)
{
if (null != sequence)
{
FastaFormatter formatter = new FastaFormatter();
parameters.Add("Query", formatter.FormatString(sequence));
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
if (!string.IsNullOrEmpty(Configuration.EmailAddress))
{
if (!parameters.Settings.ContainsKey(PARAMETEREMAIL))
{
parameters.Add(PARAMETEREMAIL, Configuration.EmailAddress);
}
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
parameters.Add(PARAMETERCOMMAND, COMMANDPUT);
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse;
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true, // do POST
parameters.Settings); // request parameters
if (!webAccessorResponse.IsSuccessful)
{
// failed
accessor.Close();
throw new Exception(String.Format(CultureInfo.InvariantCulture,
Resources.HTTPSUBMITFAILED,
webAccessorResponse.StatusDescription));
}
string info = ExtractInfoSection(webAccessorResponse.ResponseString);
if (!String.IsNullOrEmpty(info))
{
int ridStart = info.IndexOf("RID = ", StringComparison.OrdinalIgnoreCase);
if (ridStart >= 0)
{
ridStart += "RID = ".Length;
int ridEnd = info.IndexOf('\n', ridStart);
if (ridEnd >= 0)
{
requestIdentifier = info.Substring(ridStart, ridEnd - ridStart);
}
}
}
accessor.Close();
if (string.IsNullOrEmpty(requestIdentifier))
{
string message = String.Format(CultureInfo.InvariantCulture,
Resources.RIDEXTRACTFAILED,
ExtractError(webAccessorResponse.ResponseString));
throw new Exception(message);
}
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
ThreadParameter threadParameter = new ThreadParameter(
requestIdentifier,
sequence,
parameters);
// Start the BackGroundThread to check the status of job
_workerThread = new BackgroundWorker();
_workerThread.WorkerSupportsCancellation = true;
_workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
_workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
_workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}