public void TestGenBankFailureWhenParsingEmpty()
{
ISequenceParser parser = new GenBankParser();
bool failed = false;
// test ParseOne
try
{
ISequence seq = parser.ParseOne(new StringReader(string.Empty));
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for calling ParseOne on reader containing empty string.");
}
// test Parse
try
{
IList <ISequence> seqList = parser.Parse(new StringReader(string.Empty));
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for calling Parse on reader containing empty string.");
}
}
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(" ", ""));
}
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 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 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));
}
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
String inputFileName = InputFile;
GenBankParser parser = new GenBankParser();
SequenceList = parser.Parse(inputFileName);
return(ActivityExecutionStatus.Closed);
}
public void TestGenBankLocusTokenParser()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_LocusTokenParserTest).FirstOrDefault();
Assert.IsNotNull(seq);
}
public void TestGenBankParseVersionEmpty()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_ParseVersionEmpty).FirstOrDefault();
Assert.IsNotNull(seq);
}
public void TestParsingREFSEQPrimaryHeader()
{
// Test parsing Primary header which contains table with header.
// REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
GenBankParser parser = new GenBankParser(_genBankFile_WithREFSEQPrimaryData);
parser.Parse();
}
public void TestGenBankParseOriginShifted2()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_ParseOriginShifted2).FirstOrDefault();
Assert.IsNotNull(seq);
}
public void TestGenBankEmptyOrganismClassification()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_EmptyOrganismClassificationTest).FirstOrDefault();
Assert.IsNotNull(seq);
}
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 TestGenBankWhenParsingMultiple()
{
// parse
ISequenceParser parser = new GenBankParser();
IEnumerable <ISequence> seqList = parser.Parse(_multipleSeqGenBankFilename);
// Just check the number of items returned and that they're not empty. The guts
// are tested in TestGenBankWhenParsingOne.
Assert.AreEqual(2, seqList.Count());
Assert.AreEqual(105, seqList.ElementAt(0).Count);
Assert.AreEqual(5028, seqList.ElementAt(1).Count);
}
public void GenBankParserValidateParseFileName()
{
InitializeXmlVariables();
// parse
ISequenceParser parserObj = new GenBankParser();
IList <ISequence> seqList = parserObj.Parse(FilePath);
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 Parser 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 Parser 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 Parser BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, seq.ToString());
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Parser BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
}
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 GenBankParserValidateParseFileNameWithStream()
{
InitializeXmlVariables();
List <ISequence> seq = null;
IEnumerable <ISequence> seqList = null;
// Parse the Stream.
using (ISequenceParser parserObj = new GenBankParser())
{
using (StreamReader reader = new StreamReader(FilePath))
{
seqList = parserObj.Parse(reader);
seq = seqList.ToList();
}
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq[0].Alphabet);
Assert.AreEqual(SeqId, seq[0].ID);
ApplicationLog.WriteLine(
"GenBank Parser 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[0].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 Parser BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq[0].Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Parser BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
}
}
public void ValidateBasicDerivedSequenceWithGenBankFormat()
{
// Gets the expected sequence from the Xml
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGeneBankNodeName, Constants.ExpectedSequenceNode);
string geneBankFilePath = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGeneBankNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(geneBankFilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: Sequence BVT: The File exist in the Path ", geneBankFilePath));
// Parse a GenBank file Using Parse method and convert the same to sequence.
ISequenceParser parser = new GenBankParser();
IList <ISequence> sequence = parser.Parse(geneBankFilePath);
Assert.IsNotNull(sequence);
Sequence geneBankSeq = (Sequence)sequence[0];
Assert.IsNotNull(geneBankSeq);
Assert.AreEqual(expectedSequence, geneBankSeq.ToString());
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: The GenBank Sequence is as expected."));
byte[] tmpEncodedSeq = new byte[geneBankSeq.Count];
(geneBankSeq as IList <byte>).CopyTo(tmpEncodedSeq, 0);
Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: The GenBank Sequence Length is as expected."));
// Create a derived Sequences for the fastA file sequence.
BasicDerivedSequence genebankDerivedSeq =
new BasicDerivedSequence(geneBankSeq, false, false, -1, -1);
// validate the DerivedSequence with originalSequence.
Assert.IsNotNull(genebankDerivedSeq);
Assert.AreEqual(expectedSequence, genebankDerivedSeq.ToString());
Assert.AreEqual(geneBankSeq.ToString(), genebankDerivedSeq.ToString());
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: The BasicDerived Sequence is as expected."));
// Logs to Nunit GUI.
Console.WriteLine(
"Sequence BVT: Validation of GenBank file Sequence is completed successfully.");
}
public void ValidateSequenceInsertWithGenBankFormat()
{
// Gets the expected sequence from the Xml
string expectedSequenceCount = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGeneBankNodeName, Constants.SimpleFastaSequenceCount);
string geneBankFilePath = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGeneBankNodeName, Constants.FilePathNode);
string expectedSeqAfterAdd = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleGeneBankNodeName, Constants.ExpectedSeqAfterAdd);
string seqAfterAdd = string.Empty;
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string actualSequence = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.ExpectedSingleChar);
string seqBeforeAdding = string.Empty;
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Sequence BVT: Sequence {0} is expected.", actualSequence, alphabetName));
Sequence seqItem = new Sequence(Utility.GetAlphabet(alphabetName), "TCGN");
Assert.IsTrue(File.Exists(geneBankFilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Sequence BVT: The File exist in the Path {0}.", geneBankFilePath));
ISequenceParser parser = new GenBankParser();
// Parse a FastA file Using Parse method and convert the same to sequence.
IList <ISequence> sequence = parser.Parse(geneBankFilePath);
Sequence Seq = (Sequence)sequence[0];
Seq.IsReadOnly = false;
seqBeforeAdding = Seq.ToString();
Seq.Add(seqItem[0]);
// Validate sequence list after adding sequence item to the sequence list.
seqAfterAdd = Seq.ToString();
Assert.AreEqual(seqAfterAdd, expectedSeqAfterAdd);
Assert.AreNotEqual(seqAfterAdd, seqBeforeAdding);
Assert.AreEqual(Seq.Count.ToString((IFormatProvider)null), expectedSequenceCount);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Sequence BVT: Sequence {0} is expected.", seqAfterAdd));
}
public void GenBankFeatures()
{
// parse
ISequenceParser parser = new GenBankParser(_singleProteinSeqGenBankFilename);
ISequence seq = parser.Parse().FirstOrDefault();
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
List <CodingSequence> CDS = metadata.Features.CodingSequences;
Assert.AreEqual(CDS.Count, 3);
Assert.AreEqual(CDS[0].DatabaseCrossReference.Count, 1);
Assert.AreEqual(CDS[0].GeneSymbol, string.Empty);
Assert.AreEqual(metadata.Features.GetFeatures("source").Count, 1);
Assert.IsFalse(CDS[0].Pseudo);
Assert.AreEqual(metadata.GetFeatures(1, 109).Count, 2);
Assert.AreEqual(metadata.GetFeatures(1, 10).Count, 2);
Assert.AreEqual(metadata.GetFeatures(10, 100).Count, 2);
Assert.AreEqual(metadata.GetFeatures(120, 150).Count, 2);
Assert.AreEqual(metadata.GetCitationsReferredInFeatures().Count, 0);
parser.Close();
parser.Dispose();
ISequenceParser parser1 = new GenBankParser(_genBankDataPath + @"\NC_001284.gbk");
ISequence seq1 = parser1.Parse().FirstOrDefault();
metadata = seq1.Metadata["GenBank"] as GenBankMetadata;
Assert.AreEqual(metadata.Features.All.Count, 743);
Assert.AreEqual(metadata.Features.CodingSequences.Count, 117);
Assert.AreEqual(metadata.Features.Exons.Count, 32);
Assert.AreEqual(metadata.Features.Introns.Count, 22);
Assert.AreEqual(metadata.Features.Genes.Count, 60);
Assert.AreEqual(metadata.Features.MiscFeatures.Count, 455);
Assert.AreEqual(metadata.Features.Promoters.Count, 17);
Assert.AreEqual(metadata.Features.TransferRNAs.Count, 21);
Assert.AreEqual(metadata.Features.All.FindAll(F => F.Key.Equals(StandardFeatureKeys.CodingSequence)).Count, 117);
Assert.AreEqual(metadata.Features.GetFeatures(StandardFeatureKeys.CodingSequence).Count, 117);
ISequence seqTemp = metadata.Features.CodingSequences[0].GetTranslation();
byte[] tempData = new byte[seqTemp.Count];
for (int i = 0; i < seqTemp.Count; i++)
{
tempData[i] = seqTemp[i];
}
string sequenceInString = ASCIIEncoding.ASCII.GetString(tempData);
Assert.AreEqual(metadata.Features.CodingSequences[0].Translation.Trim('"'), sequenceInString.Trim('"'));
Assert.AreEqual(2, metadata.GetFeatures(11918, 12241).Count);
}
void InvalidateGenBankParser(string node)
{
// Initialization of xml strings.
FilePath = utilityObj.xmlUtil.GetTextValue(node,
Constants.FilePathNode);
try
{
GenBankParser parserObj = new GenBankParser(FilePath);
if (string.Equals(Constants.SimpleGenBankNodeName, node))
{
parserObj.LocationBuilder = null;
}
else if (string.Equals(Constants.SimpleGenBankPrimaryNode, node))
{
parserObj.Alphabet = Alphabets.RNA;
}
//parserObj.ParseOne(FilePath);
parserObj.Parse();
Assert.Fail();
}
catch (InvalidOperationException)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
catch (Exception)
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the exception:");
Console.WriteLine(
"GenBank Parser : Successfully validated the exception:");
}
}
public void TestGenBankFailureWhenParsingEmpty()
{
bool failed = false;
try
{
ISequenceParser parser = new GenBankParser();
parser.Parse();
failed = true;
}
catch (Exception)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for calling ParseOne on reader containing empty string.");
}
}
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 GenBankParserValidateParseFileName()
{
InitializeXmlVariables();
// parse
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable <ISequence> seqList = parserObj.Parse(FilePath);
ISequence seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Parser 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)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(null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine("GenBank Parser BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, seq.ConvertToString());
ApplicationLog.WriteLine("GenBank Parser BVT: Successfully validated the Sequence");
}
}
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 TestGenBankWhenUserSetsIncorrectAlphabet()
{
// parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.Protein;
bool failed = false;
try
{
var seqList = parser.Parse(_singleDnaSeqGenBankFilename);
var x = seqList.ElementAt(0);
failed = true;
}
catch (InvalidDataException)
{
// all is well with the world
}
if (failed)
{
Assert.Fail("Failed to throw exception for trying to create sequence using incorrect alphabet.");
}
}
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);
}
public void GenBankParserValidateParseOneWithSpecificFormats()
{
InitializeXmlVariables();
// Initialization of xml strings.
FilePath = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.FilePathNode);
AlphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.AlphabetNameNode);
SeqId = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.SequenceIdNode);
StrandTopology = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.StrandTopologyNode);
StrandType = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.StrandTypeNode);
Div = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.DivisionNode);
Version = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.VersionNode);
SequenceDate = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.DateNode);
PrimaryId = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.PrimaryIdNode);
ExpectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGenBankPrimaryNode,
Constants.ExpectedSequenceNode);
// parse
using (ISequenceParser parserObj = new GenBankParser(FilePath))
{
parserObj.Alphabet = Alphabets.Protein;
IEnumerable <ISequence> seq = parserObj.Parse();
Assert.AreEqual(Utility.GetAlphabet(AlphabetName),
seq.ElementAt(0).Alphabet);
Assert.AreEqual(SeqId, seq.ElementAt(0).ID);
ApplicationLog.WriteLine(
"GenBank Parser 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.ElementAt(0).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 Parser BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.ElementAt(0).Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"GenBank Parser BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Parser BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
}
}