public void ValidateSeqFormatterProperties()
{
// Gets the expected sequence from the Xml
string fastaFormatterName = this.utilityObj.xmlUtil.GetTextValue(Constants.FastAFileParserNode,
Constants.ParserNameNode);
string genBankFormatterName = this.utilityObj.xmlUtil.GetTextValue(Constants.GenBankFileParserNode,
Constants.ParserNameNode);
string gffFormatterName = this.utilityObj.xmlUtil.GetTextValue(Constants.GffFileParserNode,
Constants.ParserNameNode);
string fastQFormatterName = this.utilityObj.xmlUtil.GetTextValue(Constants.FastQFileParserNode,
Constants.ParserNameNode);
// Get SequenceFormatter class properties.
FastAFormatter actualFastAFormatter = SequenceFormatters.Fasta;
IReadOnlyList <ISequenceFormatter> allFormatters = SequenceFormatters.All;
GenBankFormatter actualgenBankFormatterName = SequenceFormatters.GenBank;
FastQFormatter actualFastQFormatterName = SequenceFormatters.FastQ;
GffFormatter actualGffFormatterName = SequenceFormatters.Gff;
// Validate Sequence Formatter
Assert.AreEqual(fastaFormatterName, actualFastAFormatter.Name);
Assert.AreEqual(genBankFormatterName, actualgenBankFormatterName.Name);
Assert.AreEqual(gffFormatterName, actualGffFormatterName.Name);
Assert.AreEqual(fastQFormatterName, actualFastQFormatterName.Name);
Assert.IsNotNull(allFormatters);
ApplicationLog.WriteLine("Type of the parser is validated successfully");
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="formatterName">Name of the formatter to use.</param>
/// <returns>If found returns the formatter as ISequenceFormatter else returns null.</returns>
public static ISequenceFormatter FindFormatterByName(string fileName, string formatterName)
{
ISequenceFormatter formatter = null;
if (!string.IsNullOrEmpty(fileName))
{
if (formatterName == Properties.Resource.FastAName)
{
formatter = new FastAFormatter(fileName);
}
else if (formatterName == Properties.Resource.FastQName)
{
formatter = new FastQFormatter(fileName);
}
else if (formatterName == Properties.Resource.GENBANK_NAME)
{
formatter = new GenBankFormatter(fileName);
}
else
{
// Do a search through the known formatters to pick up custom formatters added through add-in.
formatter = All.FirstOrDefault(p => p.Name == formatterName);
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific formatter was created for
// the passed filename - the formatter is opened automatically in the constructor.
if (formatter != null)
{
formatter.Open(fileName);
}
}
}
return(formatter);
}
public void TestGenBankForManyFiles()
{
// parser and formatter will be used for all files in input dir
// iterate through the files in input dir, parsing and formatting each; write results
// to log file
DirectoryInfo inputDirInfo = new DirectoryInfo(_genBankDataPath);
foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gbk"))
{
ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
IEnumerable <ISequence> seqList = new GenBankParser().Parse(fileInfo.FullName);
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(TempGenBankFileName))
{
(formatter as GenBankFormatter).Format(seqList.ToList());
}
using (var reader = new StreamReader(TempGenBankFileName))
{
string actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
}
}
public void TestGenBankForManyFiles()
{
// parser and formatter will be used for all files in input dir
ISequenceParser parser = new GenBankParser();
ISequenceFormatter formatter = new GenBankFormatter();
// iterate through the files in input dir, parsing and formatting each; write results
// to log file
DirectoryInfo inputDirInfo = new DirectoryInfo(_genBankDataPath);
foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gbk"))
{
ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
try
{
foreach (Sequence sequence in parser.Parse(fileInfo.FullName))
{
// don't do anything with it; just make sure it doesn't crash
formatter.FormatString(sequence);
}
ApplicationLog.WriteLine("Parse completed successfully." + Environment.NewLine);
}
catch (Exception e)
{
ApplicationLog.WriteLine("Parse failed:" + Environment.NewLine + e + Environment.NewLine);
throw;
}
}
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.Parse(_singleDnaSeqGenBankFilename).FirstOrDefault();
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(seq, TempGenBankFileName);
string actual = string.Empty;
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(Utility.CleanupWhiteSpace(_singleDnaSeqGenBankFileExpectedOutput),
Utility.CleanupWhiteSpace(actual));
}
public void GenBankFormatterValidateWriteUsingStream()
{
InitializeXmlVariables();
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
using (ISequenceParser parser1 = new GenBankParser(FilePath))
{
IEnumerable <ISequence> seqList1 = parser1.Parse();
string tempFileName = System.IO.Path.GetTempFileName();
GenBankMetadata metadata = null;
ISequence seq = null;
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
Sequence orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
(GenBankMetadata)seqList1.ElementAt(0).Metadata["GenBank"]);
orgSeq.ID = seqList1.ElementAt(0).ID;
using (ISequenceFormatter formatter = new GenBankFormatter())
{
using (StreamWriter writer = new StreamWriter(tempFileName))
{
formatter.Open(writer);
formatter.Write(orgSeq);
}
}
using (GenBankParser parserObj = new GenBankParser(tempFileName))
{
IEnumerable <ISequence> seqList = parserObj.Parse();
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
metadata = (GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString());
}
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture), metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null, "GenBank Formatter BVT: Successfully validated the Sequence '{0}'", ExpectedSequence));
File.Delete(tempFileName);
}
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser(_singleDnaSeqGenBankFilename);
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.Parse().FirstOrDefault();
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter(TempGenBankFileName);
string actual = string.Empty;
(formatter as GenBankFormatter).Write(seq);
formatter.Close();
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
/// <summary>
/// Returns formatter which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the formatter is required.</param>
/// <returns>If found returns the formatter as ISequenceFormatter else returns null.</returns>
public static ISequenceFormatter FindFormatterByFile(string fileName)
{
ISequenceFormatter formatter = null;
if (!string.IsNullOrEmpty(fileName))
{
if (Helper.IsGenBank(fileName))
{
formatter = new GenBankFormatter();
}
else if (fileName.EndsWith(Resource.GFF_FILEEXTENSION, StringComparison.InvariantCultureIgnoreCase))
{
formatter = new GffFormatter();
}
else if (Helper.IsFasta(fileName))
{
formatter = new FastaFormatter();
}
else if (Helper.IsFastQ(fileName))
{
formatter = new FastQFormatter();
}
else
{
formatter = null;
}
}
return(formatter);
}
public void ValidateSeqFormatterProperties()
{
// Gets the expected sequence from the Xml
string fastaFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.FastAFileParserNode,
Constants.ParserNameNode);
string genBankFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.GenBankFileParserNode,
Constants.ParserNameNode);
string gffFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.GffFileParserNode,
Constants.ParserNameNode);
string fastQFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.FastQFileParserNode,
Constants.ParserNameNode);
// Get SequenceFormatter class properties.
FastaFormatter actualFastAFormatter = SequenceFormatters.Fasta;
IList <ISequenceFormatter> allFormatters = SequenceFormatters.All;
GenBankFormatter actualgenBankFormatterName = SequenceFormatters.GenBank;
FastQFormatter actualFastQFormatterName = SequenceFormatters.FastQ;
GffFormatter actualGffFormatterName = SequenceFormatters.Gff;
// Validate Sequence Formatter
Assert.AreEqual(fastaFormatterName, actualFastAFormatter.Name);
Assert.AreEqual(4, allFormatters.Count);
Assert.AreEqual(genBankFormatterName, actualgenBankFormatterName.Name);
Assert.AreEqual(gffFormatterName, actualGffFormatterName.Name);
Assert.AreEqual(fastQFormatterName, actualFastQFormatterName.Name);
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceFormatter : Type of the parser is validated successfully"));
ApplicationLog.WriteLine("Type of the parser is validated successfully");
}
/// <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)
{
GenBankFormatter formatter = new GenBankFormatter();
formatter.Open(OutputFile);
if ((Sequence == null) && (SequenceList != null))
{
foreach (ISequence sequence in SequenceList)
{
formatter.Write(sequence);
}
}
else if ((Sequence != null) && (SequenceList == null))
{
formatter.Write(Sequence);
}
else if ((Sequence != null) && (SequenceList != null))
{
foreach (ISequence sequence in SequenceList)
{
formatter.Write(sequence);
}
formatter.Write(Sequence);
}
formatter.Close();
return(ActivityExecutionStatus.Closed);
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="formatterName">Name of the formatter to use.</param>
/// <returns>If found returns the formatter as ISequenceFormatter else returns null.</returns>
public static ISequenceFormatter FindFormatterByName(string fileName, string formatterName)
{
ISequenceFormatter formatter = null;
if (!string.IsNullOrEmpty(fileName))
{
if (formatterName == Properties.Resource.FastAName)
{
formatter = new FastAFormatter(fileName);
}
else if (formatterName == Properties.Resource.FastQName)
{
formatter = new FastQFormatter(fileName);
}
else if (formatterName == Properties.Resource.GENBANK_NAME)
{
formatter = new GenBankFormatter(fileName);
}
else if (formatterName == Properties.Resource.GFF_NAME)
{
formatter = new GffFormatter(fileName);
}
else
{
formatter = null;
}
}
return(formatter);
}
public void TestGenBankWhenUserSetsProteinAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.Parse(_singleProteinSeqGenBankFilename).FirstOrDefault();
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(TempGenBankFileName))
formatter.Format(seq);
string actual = string.Empty;
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", "").Replace("\r\n", Environment.NewLine), actual.Replace(" ", ""));
}
public void GenBankFormatterWithParseValidateWriteFilePath()
{
InitializeXmlVariables();
// parse
using (ISequenceParser parserObj = new GenBankParser(FilePath))
{
IEnumerable <ISequence> seqList = parserObj.Parse();
ISequence seq = seqList.ElementAt(0);
string tempFileName = System.IO.Path.GetTempFileName();
using (ISequenceFormatter formatter = new GenBankFormatter(tempFileName))
{
formatter.Write(seq);
formatter.Close();
// parse
ISequenceParser parserObjFromFile = new GenBankParser(tempFileName);
seqList = parserObjFromFile.Parse();
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata =
(GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Formatter BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
parserObjFromFile.Close();
parserObjFromFile.Dispose();
File.Delete(tempFileName);
}
}
}
public void TestGenBankWhenParsingOne()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.Parse(_singleProteinSeqGenBankFilename).FirstOrDefault();
// test the non-metadata properties
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual("SCU49845", seq.ID);
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
Assert.AreEqual(metadata.Locus.Strand, SequenceStrandType.None);
Assert.AreEqual("none", metadata.Locus.StrandTopology.ToString().ToLower(CultureInfo.CurrentCulture));
Assert.AreEqual("PLN", metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse("21-JUN-1999", (IFormatProvider)null), metadata.Locus.Date);
Assert.AreEqual("1", metadata.Version.Version);
Assert.AreEqual("1293613", metadata.Version.GiNumber);
// test that we're correctly putting all types of metadata in the right places
Assert.AreEqual(1, seq.Metadata.Count);
IList <CitationReference> referenceList = metadata.References;
Assert.AreEqual(3, referenceList.Count);
IList <FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(6, featureList.Count);
Assert.AreEqual(4, featureList[0].Qualifiers.Count);
Assert.AreEqual(5, featureList[1].Qualifiers.Count);
Assert.AreEqual(1, featureList[2].Qualifiers.Count);
// test the sequence string
string expected = @"gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgatc";
Assert.AreEqual(expected, new string(seq.Select(a => (char)a).ToArray()));
// format
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(seq, TempGenBankFileName);
string actual = string.Empty;
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
// test the formatting
Assert.AreEqual(Utility.CleanupWhiteSpace(_singleProteinSeqGenBankFileExpectedOutput),
Utility.CleanupWhiteSpace(actual));
}
public void GenBankFormatterValidateWriteWithFilePath()
{
InitializeXmlVariables();
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable <ISequence> seqList1 = parserObj.Parse(FilePath);
string tempFileName = Path.GetTempFileName();
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq = new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence)
{
ID = seqList1.ElementAt(0).ID
};
orgSeq.Metadata.Add("GenBank", seqList1.ElementAt(0).Metadata["GenBank"]);
ISequenceFormatter formatter = new GenBankFormatter();
{
formatter.Format(orgSeq, tempFileName);
// parse
ISequenceParser parserObjFromFile = new GenBankParser();
IEnumerable <ISequence> seqList = parserObjFromFile.Parse(tempFileName);
ISequence seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
var metadata =
(GenBankMetadata)orgSeq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString(null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence");
File.Delete(tempFileName);
}
}
}
public void GenBankProperties()
{
ISequenceParser parser = new GenBankParser();
Assert.AreEqual(parser.Name, Resource.GENBANK_NAME);
Assert.AreEqual(parser.Description, Resource.GENBANKPARSER_DESCRIPTION);
Assert.AreEqual(parser.SupportedFileTypes, Resource.GENBANK_FILEEXTENSION);
ISequenceFormatter formatter = new GenBankFormatter();
Assert.AreEqual(formatter.Name, Resource.GENBANK_NAME);
Assert.AreEqual(formatter.Description, Resource.GENBANKFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.SupportedFileTypes, Resource.GENBANK_FILEEXTENSION);
}
public void TestGenBankWhenParsingOne()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_singleProteinSeqGenBankFilename);
// test the non-metadata properties
Assert.IsTrue(seq.IsReadOnly);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual(MoleculeType.DNA, seq.MoleculeType);
Assert.AreEqual("SCU49845", seq.DisplayID);
Assert.AreEqual("SCU49845", seq.ID);
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
Assert.AreEqual(metadata.Locus.Strand, SequenceStrandType.None);
Assert.AreEqual("none", metadata.Locus.StrandTopology.ToString().ToLower());
Assert.AreEqual("PLN", metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse("21-JUN-1999"), metadata.Locus.Date);
Assert.AreEqual("1", metadata.Version.Version);
Assert.AreEqual("1293613", metadata.Version.GINumber);
// test that we're correctly putting all types of metadata in the right places
Assert.AreEqual(1, seq.Metadata.Count);
IList <CitationReference> referenceList = metadata.References;
Assert.AreEqual(3, referenceList.Count);
IList <FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(6, featureList.Count);
Assert.AreEqual(4, featureList[0].Qualifiers.Count);
Assert.AreEqual(5, featureList[1].Qualifiers.Count);
Assert.AreEqual(1, featureList[2].Qualifiers.Count);
// test the sequence string
string expected = @"GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGTTACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAACATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAGACGCGAAAAAAAAAGAACAACGCGTCATAGAACTTTTGGCAATTCGCGTCACAAATAAATTTTGGCAACTTATGTTTCCTCTTCGAGCAGTACTCGAGCCCTGTCTCAAGAATGTAATAATACCCATCGTAGGTATGGTTAAAGATAGCATCTCCACAACCTCAAAGCTCCTTGCCGAGAGTCGCCCTCCTTTGTCGAGTAATTTTCACTTTTCATATGAGAACTTATTTTCTTATTCTTTACTCTCACATCCTGTAGTGATTGACACTGCAACAGCCACCATCACTAGAAGAACAGAACAATTACTTAATAGAAAAATTATATCTTCCTCGAAACGATTTCCTGCTTCCAACATCTACGTATATCAAGAAGCATTCACTTACCATGACACAGCTTCAGATTTCATTATTGCTGACAGCTACTATATCACTACTCCATCTAGTAGTGGCCACGCCCTATGAGGCATATCCTATCGGAAAACAATACCCCCCAGTGGCAAGAGTCAATGAATCGTTTACATTTCAAATTTCCAATGATACCTATAAATCGTCTGTAGACAAGACAGCTCAAATAACATACAATTGCTTCGACTTACCGAGCTGGCTTTCGTTTGACTCTAGTTCTAGAACGTTCTCAGGTGAACCTTCTTCTGACTTACTATCTGATGCGAACACCACGTTGTATTTCAATGTAATACTCGAGGGTACGGACTCTGCCGACAGCACGTCTTTGAACAATACATACCAATTTGTTGTTACAAACCGTCCATCCATCTCGCTATCGTCAGATTTCAATCTATTGGCGTTGTTAAAAAACTATGGTTATACTAACGGCAAAAACGCTCTGAAACTAGATCCTAATGAAGTCTTCAACGTGACTTTTGACCGTTCAATGTTCACTAACGAAGAATCCATTGTGTCGTATTACGGACGTTCTCAGTTGTATAATGCGCCGTTACCCAATTGGCTGTTCTTCGATTCTGGCGAGTTGAAGTTTACTGGGACGGCACCGGTGATAAACTCGGCGATTGCTCCAGAAACAAGCTACAGTTTTGTCATCATCGCTACAGACATTGAAGGATTTTCTGCCGTTGAGGTAGAATTCGAATTAGTCATCGGGGCTCACCAGTTAACTACCTCTATTCAAAATAGTTTGATAATCAACGTTACTGACACAGGTAACGTTTCATATGACTTACCTCTAAACTATGTTTATCTCGATGACGATCCTATTTCTTCTGATAAATTGGGTTCTATAAACTTATTGGATGCTCCAGACTGGGTGGCATTAGATAATGCTACCATTTCCGGGTCTGTCCCAGATGAATTACTCGGTAAGAACTCCAATCCTGCCAATTTTTCTGTGTCCATTTATGATACTTATGGTGATGTGATTTATTTCAACTTCGAAGTTGTCTCCACAACGGATTTGTTTGCCATTAGTTCTCTTCCCAATATTAACGCTACAAGGGGTGAATGGTTCTCCTACTATTTTTTGCCTTCTCAGTTTACAGACTACGTGAATACAAACGTTTCATTAGAGTTTACTAATTCAAGCCAAGACCATGACTGGGTGAAATTCCAATCATCTAATTTAACATTAGCTGGAGAAGTGCCCAAGAATTTCGACAAGCTTTCATTAGGTTTGAAAGCGAACCAAGGTTCACAATCTCAAGAGCTATATTTTAACATCATTGGCATGGATTCAAAGATAACTCACTCAAACCACAGTGCGAATGCAACGTCCACAAGAAGTTCTCACCACTCCACCTCAACAAGTTCTTACACATCTTCTACTTACACTGCAAAAATTTCTTCTACCTCCGCTGCTGCTACTTCTTCTGCTCCAGCAGCGCTGCCAGCAGCCAATAAAACTTCATCTCACAATAAAAAAGCAGTAGCAATTGCGTGCGGTGTTGCTATCCCATTAGGCGTTATCCTAGTAGCTCTCATTTGCTTCCTAATATTCTGGAGACGCAGAAGGGAAAATCCAGACGATGAAAACTTACCGCATGCTATTAGTGGACCTGATTTGAATAATCCTGCAAATAAACCAAATCAAGAAAACGCTACACCTTTGAACAACCCCTTTGATGATGATGCTTCCTCGTACGATGATACTTCAATAGCAAGAAGATTGGCTGCTTTGAACACTTTGAAATTGGATAACCACTCTGCCACTGAATCTGATATTTCCAGCGTGGATGAAAAGAGAGATTCTCTATCAGGTATGAATACATACAATGATCAGTTCCAATCCCAAAGTAAAGAAGAATTATTAGCAAAACCCCCAGTACAGCCTCCAGAGAGCCCGTTCTTTGACCCACAGAATAGGTCTTCTTCTGTGTATATGGATAGTGAACCAGCAGTAAATAAATCCTGGCGATATACTGGCAACCTGTCACCAGTCTCTGATATTGTCAGAGACAGTTACGGATCACAAAAAACTGTTGATACAGAAAAACTTTTCGATTTAGAAGCACCAGAGAAGGAAAAACGTACGTCAAGGGATGTCACTATGTCTTCACTGGACCCTTGGAACAGCAATATTAGCCCTTCTCCCGTAAGAAAATCAGTAACACCATCACCATATAACGTAACGAAGCATCGTAACCGCCACTTACAAAATATTCAAGACTCTCAAAGCGGTAAAAACGGAATCACTCCCACAACAATGTCAACTTCATCTTCTGACGATTTTGTTCCGGTTAAAGATGGTGAAAATTTTTGCTGGGTCCATAGCATGGAACCAGACAGAAGACCAAGTAAGAAAAGGTTAGTAGATTTTTCAAATAAGAGTAATGTCAATGTTGGTCAAGTTAAGGACATTCACGGACGCATCCCAGAAATGCTGTGATTATACGCAACGATATTTTGCTTAATTTTATTTTCCTGTTTTATTTTTTATTAGTGGTTTACAGATACCCTATATTTTATTTAGTTTTTATACTTAGAGACATTTAATTTTAATTCCATTCTTCAAATTTCATTTTTGCACTTAAAACAAAGATCCAAAAATGCTCTCGCCCTCTTCATATTGAGAATACACTCCATTCAAAATTTTGTCGTCACCGCTGATTAATTTTTCACTAAACTGATGAATAATCAAAGGCCCCACGTCAGAACCGACTAAAGAAGTGAGTTTTATTTTAGGAGGTTGAAAACCATTATTGTCTGGTAAATTTTCATCTTCTTGACATTTAACCCAGTTTGAATCCCTTTCAATTTCTGCTTTTTCCTCCAAACTATCGACCCTCCTGTTTCTGTCCAACTTATGTCCTAGTTCCAATTCGATCGCATTAATAACTGCTTCAAATGTTATTGTGTCATCGTTGACTTTAGGTAATTTCTCCAAATGCATAATCAAACTATTTAAGGAAGATCGGAATTCGTCGAACACTTCAGTTTCCGTAATGATCTGATCGTCTTTATCCACATGTTGTAATTCACTAAAATCTAAAACGTATTTTTCAATGCATAAATCGTTCTTTTTATTAATAATGCAGATGGAAAATCTGTAAACGTGCGTTAATTTAGAAAGAACATCCAGTATAAGTTCTTCTATATAGTCAATTAAAGCAGGATGCCTATTAATGGGAACGAACTGCGGCAAGTTGAATGACTGGTAAGTAGTGTAGTCGAATGACTGAGGTGGGTATACATTTCTATAAAATAAAATCAAATTAATGTAGCATTTTAAGTATACCCTCAGCCACTTCTCTACCCATCTATTCATAAAGCTGACGCAACGATTACTATTTTTTTTTTCTTCTTGGATCTCAGTCGTCGCAAAAACGTATACCTTCTTTTTCCGACCTTTTTTTTAGCTTTCTGGAAAAGTTTATATTAGTTAAACAGGGTCTAGTCTTAGTGTGAAAGCTAGTGGTTTCGATTGACTGATATTAAGAAAGTGGAAATTAAATTAGTAGTGTAGACGTATATGCATATGTATTTCTCGCCTGTTTATGTTTCTACGTACTTTTGATTTATAGCAAGGGGAAAAGAAATACATACTATTTTTTGGTAAAGGTGAAAGCATAATGTAAAAGCTAGAATAAAATGGACGAAATAAAGAGAGGCTTAGTTCATCTTTTTTCCAAAAAGCACCCAATGATAATAACTAAAATGAAAAGGATTTGCCATCTGTCAGCAACATCAGTTGTGTGAGCAATAATAAAATCATCACCTCCGTTGCCTTTAGCGCGTTTGTCGTTTGTATCTTCCGTAATTTTAGTCTTATCAATGGGAATCATAAATTTTCCAATGAATTAGCAATTTCGTCCAATTCTTTTTGAGCTTCTTCATATTTGCTTTGGAATTCTTCGCACTTCTTTTCCCATTCATCTCTTTCTTCTTCCAAAGCAACGATCCTTCTACCCATTTGCTCAGAGTTCAAATCGGCCTCTTTCAGTTTATCCATTGCTTCCTTCAGTTTGGCTTCACTGTCTTCTAGCTGTTGTTCTAGATCCTGGTTTTTCTTGGTGTAGTTCTCATTATTAGATCTCAAGTTATTGGAGTCTTCAGCCAATTGCTTTGTATCAGACAATTGACTCTCTAACTTCTCCACTTCACTGTCGAGTTGCTCGTTTTTAGCGGACAAAGATTTAATCTCGTTTTCTTTTTCAGTGTTAGATTGCTCTAATTCTTTGAGCTGTTCTCTCAGCTCCTCATATTTTTCTTGCCATGACTCAGATTCTAATTTTAAGCTATTCAATTTCTCTTTGATC";
Assert.AreEqual(expected, seq.ToString());
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.ParseOne(_singleDnaSeqGenBankFilename);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
/// <summary>
/// Returns formatter which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the formatter is required.</param>
/// <returns>If found returns the formatter as ISequenceFormatter else returns null.</returns>
public static ISequenceFormatter FindFormatterByFileName(string fileName)
{
ISequenceFormatter formatter = null;
if (!string.IsNullOrEmpty(fileName))
{
if (IsFasta(fileName))
{
formatter = new FastAFormatter(fileName);
}
else if (IsFastQ(fileName))
{
formatter = new FastQFormatter(fileName);
}
else if (IsGenBank(fileName))
{
formatter = new GenBankFormatter(fileName);
}
else if (fileName.EndsWith(Properties.Resource.GFF_FILEEXTENSION, StringComparison.InvariantCultureIgnoreCase))
{
formatter = new GffFormatter(fileName);
}
else
{
// Do a search through the known formatters to pick up custom formatters added through add-in.
string fileExtension = Path.GetExtension(fileName);
if (!string.IsNullOrEmpty(fileExtension))
{
formatter = All.FirstOrDefault(p => p.SupportedFileTypes.Contains(fileExtension));
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific formatter was created for
// the passed filename - the formatter is opened automatically in the constructor.
if (formatter != null)
{
formatter.Open(fileName);
}
}
}
}
return(formatter);
}
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
GenBankFormatter formatter = new GenBankFormatter();
if ((Sequence == null) && (SequenceList != null))
{
formatter.Format(SequenceList, OutputFile);
}
else if ((Sequence != null) && (SequenceList == null))
{
formatter.Format(Sequence, OutputFile);
}
else if ((Sequence != null) && (SequenceList != null))
{
SequenceList.Add(Sequence);
formatter.Format(SequenceList, OutputFile);
SequenceList.Remove(Sequence);
}
return(ActivityExecutionStatus.Closed);
}
public void TestGenBankForManyFiles()
{
// parser and formatter will be used for all files in input dir
// iterate through the files in input dir, parsing and formatting each; write results
// to log file
DirectoryInfo inputDirInfo = new DirectoryInfo(_genBankDataPath);
foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gbk"))
{
ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
ISequenceParser parser = new GenBankParser(fileInfo.FullName);
try
{
IEnumerable <ISequence> seqList = parser.Parse();
// don't do anything with it; just make sure it doesn't crash
ISequenceFormatter formatter = new GenBankFormatter(TempGenBankFileName);
string actual = string.Empty;
(formatter as GenBankFormatter).Write(seqList.ToList());
using (StreamReader reader = new StreamReader(TempGenBankFileName))
{
actual = reader.ReadToEnd();
}
File.Delete(TempGenBankFileName);
parser.Close();
parser.Dispose();
ApplicationLog.WriteLine("Parse completed successfully." + Environment.NewLine);
}
catch (Exception e)
{
ApplicationLog.WriteLine("Parse failed:" + Environment.NewLine + e + Environment.NewLine);
throw;
}
}
}
public void GenBankFormatterValidateReadAndWriteMultipleDBLinks()
{
// Create a Sequence with all attributes.
// parse and update the properties instead of parsing entire file.
string tempFileName = Path.GetTempFileName();
ISequenceParser parser1 = new GenBankParser();
using (parser1.Open(_genBankFile_WithMultipleDBLines))
{
var orgSeq = parser1.Parse().First();
ISequenceFormatter formatter = new GenBankFormatter();
using (formatter.Open(tempFileName))
{
formatter.Format(orgSeq);
formatter.Close();
}
}
var same = Utility.CompareFiles(tempFileName, _genBankFile_WithMultipleDBLines);
File.Delete(tempFileName);
Assert.IsTrue(same);
ApplicationLog.WriteLine("GenBank Formatter: Successful read->write loop");
}
public void GenBankFormatterWithParseValidateFormatFilePath()
{
InitializeXmlVariables();
// parse
ISequenceParser parserObj = new GenBankParser();
IList <ISequence> seqList = parserObj.Parse(FilePath);
ISequence seq = seqList[0];
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(seq, Constants.GenBankTempFileName);
// parse
parserObj = new GenBankParser();
seqList = parserObj.Parse(Constants.GenBankTempFileName);
seq = seqList[0];
// test the non-metadata properties
if (0 == string.Compare(IsSequenceReadOnly, "true",
false, CultureInfo.CurrentCulture))
{
Assert.IsTrue(seq.IsReadOnly);
ApplicationLog.WriteLine("Successfully validated the ReadOnly Property");
}
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(Utility.GetMoleculeType(MolType), seq.MoleculeType);
Assert.AreEqual(SeqId, seq.DisplayID);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata =
(GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GINumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, seq.ToString());
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Formatter BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
File.Delete(Constants.GenBankTempFileName);
}
public void GenBankFormatterValidateFormatTextWriter()
{
InitializeXmlVariables();
// Create a Sequence with all attributes.
// parse and update the properties instead of parsing entire file.
ISequenceParser parser1 = new GenBankParser();
IList <ISequence> seqList1 = parser1.Parse(FilePath);
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
Sequence orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
(GenBankMetadata)seqList1[0].Metadata["GenBank"]);
orgSeq.ID = seqList1[0].ID;
orgSeq.DisplayID = seqList1[0].DisplayID;
orgSeq.MoleculeType = seqList1[0].MoleculeType;
ISequenceFormatter formatter = new GenBankFormatter();
using (TextWriter writer =
new StreamWriter(Constants.GenBankTempFileName))
{
formatter.Format(orgSeq, writer);
}
// parse
GenBankParser parserObj = new GenBankParser();
IList <ISequence> seqList = parserObj.Parse(Constants.GenBankTempFileName);
ISequence seq = seqList[0];
// test the non-metadata properties
if (0 == string.Compare(IsSequenceReadOnly, "true",
false, CultureInfo.CurrentCulture))
{
Assert.IsTrue(seq.IsReadOnly);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the ReadOnly Property");
}
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(Utility.GetMoleculeType(MolType), seq.MoleculeType);
Assert.AreEqual(SeqId, seq.DisplayID);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture), metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GINumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, seq.ToString());
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null, "GenBank Formatter BVT: Successfully validated the Sequence '{0}'", ExpectedSequence));
File.Delete(Constants.GenBankTempFileName);
}