/// <summary>
/// Reads the Genbank file and have it parsed by MBF library.
/// </summary>
/// <param name="genbankFileURL">Your genbank file path</param>
/// <returns></returns>
private SequenceList ParseSequencePath
(string genbankFileURL)
{
if (IsOnline)
throw new NotImplementedException
("online genbank reading is not supported in this version!");
//Download the file and parse it
//Create the parser first
ISequenceParser gbParser = new GenBankParser();
//Always Try parsing multi sequence in a file
List<ISequence> mbfSequences = gbParser.Parse(genbankFileURL);
SequenceList bioSeqList = new SequenceList();
foreach (Sequence mbfseq in mbfSequences)
{
ConvertToBioPatMLSeq(mbfseq);
bioSeqList.Add(ConvertToBioPatMLSeq(mbfseq));
}
return bioSeqList;
}
private static void initiate_Updater()
{
int i = 1;
Console.WriteLine("Connecting to database prokaryote_schema...");
try
{
conn = new MySqlConnection("Server=127.0.0.1;Database=prokaryote_schema;Uid=root;Pwd=Anitar@n@");
conn.Open();
Console.WriteLine("Connected to database prokaryote_schema\n");
newbacteriaspath = new List <string>();
extract_newbacterias();
Console.WriteLine("\nNumber of bacterias to be parsed to database: {0}\n", newbacteriaspath.Count);
Console.WriteLine("Press any key to initiate the parsing");
Console.ReadKey();
Console.WriteLine("Loading newbacterias to database...");
foreach (var bacteria in newbacteriaspath)
{
Console.WriteLine("Parsing .gbff file [{0}/{1}]", i, newbacteriaspath.Count);
List <ISequence> sequences = new List <ISequence>();
ISequenceParser parser = new Bio.IO.GenBank.GenBankParser();
using (parser.Open(bacteria))
{
sequences = parser.Parse().ToList();
}
int j = 1;
foreach (var sequence in sequences)
{
Console.WriteLine("\tParsingSequence [{0}/{1}]", j, sequences.Count);
parse_to_database(sequence);
j++;
}
Console.WriteLine();
append_new_path(bacteria);
i++;
prokaryote_id = 0;
}
}
catch (Exception ex)
{
Console.WriteLine("\nError occured: " + ex.Message);
}
finally
{
if (i - 1 == newbacteriaspath.Count && newbacteriaspath.Count != 0)
{
Console.WriteLine("\nDatabase Updated Successfully");
}
else
{
Console.WriteLine("\nDatabase is not Updated");
}
}
}
//this functiion parses the data from .gbff file
private void extract_sequences()
{
ISequenceParser parser = new Bio.IO.GenBank.GenBankParser();
//Console.WriteLine(path);
using (parser.Open(this.path))
{
this.sequences = parser.Parse().ToList();
}
}
/// <summary>
/// The param could also be a stringreader.
/// </summary>
/// <param name="reader"></param>
/// <returns></returns>
private SequenceList ParseSequencePath
(TextReader reader)
{
//Create the parser first
ISequenceParser gbParser = new GenBankParser();
//Always Try parsing multi sequence in a reader
List<ISequence> mbfSequences = gbParser.Parse(reader);
SequenceList bioSeqList = new SequenceList();
foreach (Sequence mbfseq in mbfSequences)
{
ConvertToBioPatMLSeq(mbfseq);
bioSeqList.Add(ConvertToBioPatMLSeq(mbfseq));
}
return bioSeqList;
}
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 = CompareFiles(tempFileName, _genBankFile_WithMultipleDBLines);
File.Delete(tempFileName);
Assert.IsTrue(same);
ApplicationLog.WriteLine("GenBank Formatter: Successful read->write loop");
}
public void GenBankFeatures()
{
// parse
ISequence seq = new GenBankParser()
.Parse(_singleProteinSeqGenBankFilename)
.FirstOrDefault();
Assert.IsNotNull(seq);
GenBankMetadata metadata = seq.Metadata["GenBank"] as GenBankMetadata;
Assert.IsNotNull(metadata);
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);
ISequence seq1 = new GenBankParser()
.Parse(_genBankDataPath + @"\NC_001284.gbk")
.FirstOrDefault();
Assert.IsNotNull(seq1);
metadata = seq1.Metadata["GenBank"] as GenBankMetadata;
Assert.IsNotNull(metadata);
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 = Encoding.ASCII.GetString(tempData);
Assert.AreEqual(metadata.Features.CodingSequences[0].Translation.Trim('"'), sequenceInString.Trim('"'));
Assert.AreEqual(2, metadata.GetFeatures(11918, 12241).Count);
}
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 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(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", "").Replace("\r\n", Environment.NewLine), actual.Replace(" ", ""));
}
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(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", "").Replace("\r\n", Environment.NewLine), actual.Replace(" ", ""));
}
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);
}
/// <summary>
/// Validate GenBank Get features with specified range.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">name of method</param>
private void ValidateGetFeatures(string nodeName, string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedFirstRangeStartPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstRangeStartPoint);
string expectedSecondRangeStartPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondRangeStartPoint);
string expectedFirstRangeEndPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstRangeEndPoint);
string expectedSecondRangeEndPoint = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondRangeEndPoint);
string expectedCountWithinSecondRange = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FeaturesWithinSecondRange);
string expectedCountWithinFirstRange = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FeaturesWithinFirstRange);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
var metadata =
seq.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
List<CodingSequence> cdsList = metadata.Features.CodingSequences;
string accessionNumber = cdsList[0].Location.Accession;
if ((0 == string.Compare(methodName, "Accession",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
// Validate GetFeature within specified range.
Assert.AreEqual(metadata.GetFeatures(accessionNumber,
Convert.ToInt32(expectedFirstRangeStartPoint, null),
Convert.ToInt32(expectedFirstRangeEndPoint, null))
.Count.ToString((IFormatProvider) null),
expectedCountWithinFirstRange);
Assert.AreEqual(metadata.GetFeatures(accessionNumber,
Convert.ToInt32(expectedSecondRangeStartPoint, null),
Convert.ToInt32(expectedSecondRangeEndPoint, null))
.Count.ToString((IFormatProvider) null),
expectedCountWithinSecondRange);
}
else
{
// Validate GetFeature within specified range.
Assert.AreEqual(metadata.GetFeatures(
Convert.ToInt32(expectedFirstRangeStartPoint, null),
Convert.ToInt32(expectedFirstRangeEndPoint, null)).Count.ToString((IFormatProvider) null),
expectedCountWithinFirstRange);
Assert.AreEqual(metadata.GetFeatures(
Convert.ToInt32(expectedSecondRangeStartPoint, null),
Convert.ToInt32(expectedSecondRangeEndPoint, null)).Count.ToString((IFormatProvider) null),
expectedCountWithinSecondRange);
}
}
}
public void GenBankFormatterValidateWriteUsingStream()
{
InitializeXmlVariables();
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
ISequenceParser parser1 = new GenBankParser();
{
IEnumerable<ISequence> seqList1 = parser1.Parse(FilePath);
string tempFileName = Path.GetTempFileName();
GenBankMetadata metadata = null;
ISequence seq = null;
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
seqList1.ElementAt(0).Metadata["GenBank"]);
orgSeq.ID = seqList1.ElementAt(0).ID;
ISequenceFormatter formatter = new GenBankFormatter();
{
using (formatter.Open(tempFileName))
{
formatter.Format(orgSeq);
}
}
var parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
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(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 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
ISequenceParser parserObj = new GenBankParser();
{
parserObj.Alphabet = Alphabets.Protein;
IEnumerable<ISequence> seq = parserObj.Parse(FilePath);
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
var 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(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");
}
}
/// <summary>
/// Validates GenBank Formatter for General test cases.
/// </summary>
/// <param name="seqList">sequence list.</param>
private static void ValidateWriteGeneralTestCases(IEnumerable<ISequence> seqList1)
{
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
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;
string tempFileName = System.IO.Path.GetTempFileName();
ISequenceFormatter formatter = new GenBankFormatter();
formatter.Format(orgSeq, tempFileName);
// parse
GenBankParser parserObj = new GenBankParser();
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
ISequence seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter P1: 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());
}
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
}
if (metadata.Locus.DivisionCode != SequenceDivisionCode.None)
{
Assert.AreEqual(Div,
metadata.Locus.DivisionCode.ToString());
}
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
if (0 != string.Compare(AlphabetName, "rna",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
{
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
}
else
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date Properties");
}
string truncatedExpectedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
string truncatedActualSequence =
new string(seq.Select(a => (char)a).ToArray()).Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
// test the sequence string
Assert.AreEqual(truncatedExpectedSequence, truncatedActualSequence);
ApplicationLog.WriteLine(
"GenBank Formatter P1: Successfully validated the Sequence");
File.Delete(tempFileName);
}
public void TestGenBankLocusTokenParser()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_LocusTokenParserTest).FirstOrDefault();
Assert.IsNotNull(seq);
}
/// <summary>
/// Validate GenBank Citation referenced by passing featureItem present in GenBank Metadata.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateCitationReferencedUsingFeatureItem(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedCitationReferenced = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.citationReferencedCount);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
var metadata =
seq.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
IList<FeatureItem> featureList = metadata.Features.All;
// Get a list citationReferenced present in GenBank file.
List<CitationReference> citationReferenceList =
metadata.GetCitationsReferredInFeature(featureList[0]);
Assert.AreEqual(citationReferenceList.Count.ToString((IFormatProvider) null),
expectedCitationReferenced);
}
}
public void TestGenBankParseVersionEmpty()
{
// parse
GenBankParser parser = new GenBankParser();
ISequence seq = parser.Parse(_genBankFile_ParseVersionEmpty).FirstOrDefault();
Assert.IsNotNull(seq);
}
/// <summary>
/// Validate All qualifiers in CDS feature.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateCDSQualifiers(string nodeName, string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedCDSProduct = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSProductQualifier);
string expectedCDSException = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSException);
string expectedCDSCodonStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCodonStart);
string expectedCDSLabel = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSLabel);
string expectedCDSDBReference = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSDBReference);
string expectedGeneSymbol = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneSymbol);
// Parse a GenBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
var metadata =
seq.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
// Get CDS qaulifier.value.
List<CodingSequence> cdsQualifiers = metadata.Features.CodingSequences;
List<string> codonStartValue = cdsQualifiers[0].CodonStart;
List<string> productValue = cdsQualifiers[0].Product;
List<string> DBReferenceValue = cdsQualifiers[0].DatabaseCrossReference;
// validate CDS qualifiers.
if ((0 == string.Compare(methodName, "DNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
|| (0 == string.Compare(methodName, "RNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
Assert.AreEqual(cdsQualifiers[0].Label,
expectedCDSLabel);
Assert.AreEqual(cdsQualifiers[0].Exception.ToString(null),
expectedCDSException);
Assert.AreEqual(productValue[0],
expectedCDSProduct);
Assert.AreEqual(codonStartValue[0],
expectedCDSCodonStart);
Assert.IsTrue(string.IsNullOrEmpty(cdsQualifiers[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(cdsQualifiers[0].Citation.ToString()));
Assert.AreEqual(DBReferenceValue[0],
expectedCDSDBReference);
Assert.AreEqual(cdsQualifiers[0].GeneSymbol,
expectedGeneSymbol);
}
else
{
Assert.AreEqual(cdsQualifiers[0].Label, expectedCDSLabel);
Assert.AreEqual(cdsQualifiers[0].Exception.ToString(null), expectedCDSException);
Assert.IsTrue(string.IsNullOrEmpty(cdsQualifiers[0].Allele));
Assert.IsFalse(string.IsNullOrEmpty(cdsQualifiers[0].Citation.ToString()));
Assert.AreEqual(DBReferenceValue[0], expectedCDSDBReference);
Assert.AreEqual(cdsQualifiers[0].GeneSymbol, expectedGeneSymbol);
}
}
}
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.");
}
}
/// <summary>
/// Validate Seqeunce feature of GenBank file.
/// </summary>
/// <param name="nodeName">xml node name. for different alphabet</param>
private void ValidateSequenceFeature(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string subSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSubSequence);
string subSequenceStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceStart);
string subSequenceEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceEnd);
ISequence firstFeatureSeq = null;
// Parse a genBank file.
ISequenceParser parserObj = new GenBankParser();
{
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
var metadata = seq.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
// Get Subsequence feature,start and end postions.
firstFeatureSeq = metadata.Features.All[0].GetSubSequence(seq.ElementAt(0));
var sequenceString = new string(firstFeatureSeq.Select(a => (char) a).ToArray());
// Validate SubSequence.
Assert.AreEqual(sequenceString, subSequence);
Assert.AreEqual(metadata.Features.All[0].Location.LocationStart.ToString((IFormatProvider) null),
subSequenceStart);
Assert.AreEqual(metadata.Features.All[0].Location.LocationEnd.ToString((IFormatProvider) null),
subSequenceEnd);
Assert.IsNull(metadata.Features.All[0].Location.Accession);
Assert.AreEqual(metadata.Features.All[0].Location.StartData,
subSequenceStart);
Assert.AreEqual(metadata.Features.All[0].Location.EndData,
subSequenceEnd);
}
}
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 ValidateGenBankFeatureProperties()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.FilePathNode);
string mRNAFeatureCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.mRNACount);
string exonFeatureCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.ExonCount);
string intronFeatureCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.IntronCount);
string cdsFeatureCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.CDSCount);
string allFeaturesCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.GenBankFeaturesCount);
string GenesCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.GeneCount);
string miscFeaturesCount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.MiscFeatureCount);
string rRNACount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.rRNACount);
string tRNACount = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.tRNACount);
string zeroValue = utilityObj.xmlUtil.GetTextValue(
Constants.DNAStandardFeaturesKeyNode, Constants.emptyCount);
ISequenceParser parserObj = new GenBankParser();
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
// Get all metada features. Hitting all the properties in the metadata feature.
var metadata = (GenBankMetadata) seq.ElementAt(0).Metadata[Constants.GenBank];
List<FeatureItem> allFeatures = metadata.Features.All;
List<Minus10Signal> minus10Signal = metadata.Features.Minus10Signals;
List<Minus35Signal> minus35Signal = metadata.Features.Minus35Signals;
List<ThreePrimeUtr> threePrimeUTR = metadata.Features.ThreePrimeUTRs;
List<FivePrimeUtr> fivePrimeUTR = metadata.Features.FivePrimeUTRs;
List<Attenuator> attenuator = metadata.Features.Attenuators;
List<CaatSignal> caatSignal = metadata.Features.CAATSignals;
List<CodingSequence> CDS = metadata.Features.CodingSequences;
List<DisplacementLoop> displacementLoop = metadata.Features.DisplacementLoops;
List<Enhancer> enhancer = metadata.Features.Enhancers;
List<Exon> exonList = metadata.Features.Exons;
List<GcSingal> gcsSignal = metadata.Features.GCSignals;
List<Gene> genesList = metadata.Features.Genes;
List<InterveningDna> interveningDNA = metadata.Features.InterveningDNAs;
List<Intron> intronList = metadata.Features.Introns;
List<LongTerminalRepeat> LTR = metadata.Features.LongTerminalRepeats;
List<MaturePeptide> matPeptide = metadata.Features.MaturePeptides;
List<MiscBinding> miscBinding = metadata.Features.MiscBindings;
List<MiscDifference> miscDifference = metadata.Features.MiscDifferences;
List<MiscFeature> miscFeatures = metadata.Features.MiscFeatures;
List<MiscRecombination> miscRecobination =
metadata.Features.MiscRecombinations;
List<MiscRna> miscRNA = metadata.Features.MiscRNAs;
List<MiscSignal> miscSignal = metadata.Features.MiscSignals;
List<MiscStructure> miscStructure = metadata.Features.MiscStructures;
List<ModifiedBase> modifierBase = metadata.Features.ModifiedBases;
List<MessengerRna> mRNA = metadata.Features.MessengerRNAs;
List<NonCodingRna> nonCodingRNA = metadata.Features.NonCodingRNAs;
List<OperonRegion> operonRegion = metadata.Features.OperonRegions;
List<PolyASignal> polySignal = metadata.Features.PolyASignals;
List<PolyASite> polySites = metadata.Features.PolyASites;
List<PrecursorRna> precursorRNA = metadata.Features.PrecursorRNAs;
List<ProteinBindingSite> proteinBindingSites =
metadata.Features.ProteinBindingSites;
List<RibosomeBindingSite> rBindingSites =
metadata.Features.RibosomeBindingSites;
List<ReplicationOrigin> repliconOrigin =
metadata.Features.ReplicationOrigins;
List<RepeatRegion> repeatRegion = metadata.Features.RepeatRegions;
List<RibosomalRna> rRNA = metadata.Features.RibosomalRNAs;
List<SignalPeptide> signalPeptide = metadata.Features.SignalPeptides;
List<StemLoop> stemLoop = metadata.Features.StemLoops;
List<TataSignal> tataSignals = metadata.Features.TATASignals;
List<Terminator> terminator = metadata.Features.Terminators;
List<TransferMessengerRna> tmRNA =
metadata.Features.TransferMessengerRNAs;
List<TransitPeptide> transitPeptide = metadata.Features.TransitPeptides;
List<TransferRna> tRNA = metadata.Features.TransferRNAs;
List<UnsureSequenceRegion> unSecureRegion =
metadata.Features.UnsureSequenceRegions;
List<Variation> variations = metadata.Features.Variations;
// Validate GenBank Features.
Assert.AreEqual(minus10Signal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(minus35Signal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(threePrimeUTR.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(fivePrimeUTR.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(caatSignal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(attenuator.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(displacementLoop.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(enhancer.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(gcsSignal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(genesList.Count.ToString((IFormatProvider) null), GenesCount);
Assert.AreEqual(interveningDNA.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(LTR.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(matPeptide.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscBinding.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscDifference.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscFeatures.Count.ToString((IFormatProvider) null), miscFeaturesCount);
Assert.AreEqual(miscRecobination.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscSignal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(modifierBase.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscRNA.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(miscStructure.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(mRNA.Count.ToString((IFormatProvider) null), mRNAFeatureCount);
Assert.AreEqual(nonCodingRNA.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(operonRegion.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(polySignal.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(polySites.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(precursorRNA.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(proteinBindingSites.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(rBindingSites.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(repliconOrigin.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(rRNA.Count.ToString((IFormatProvider) null), rRNACount);
Assert.AreEqual(signalPeptide.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(stemLoop.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(tataSignals.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(repeatRegion.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(terminator.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(tmRNA.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(variations.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(tRNA.Count.ToString((IFormatProvider) null), tRNACount);
Assert.AreEqual(transitPeptide.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(unSecureRegion.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(stemLoop.Count, Convert.ToInt32(zeroValue, null));
Assert.AreEqual(allFeatures.Count, Convert.ToInt32(allFeaturesCount, null));
Assert.AreEqual(CDS.Count, Convert.ToInt32(cdsFeatureCount, null));
Assert.AreEqual(exonList.Count, Convert.ToInt32(exonFeatureCount, null));
Assert.AreEqual(intronList.Count, Convert.ToInt32(intronFeatureCount, null));
}
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 ValidateSequenceFeatureUsingReferencedSequence()
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankFileSubSequenceNode, Constants.FilePathNode);
string subSequence = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankFileSubSequenceNode, Constants.ExpectedSubSequence);
string subSequenceStart = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankFileSubSequenceNode, Constants.SequenceStart);
string subSequenceEnd = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankFileSubSequenceNode, Constants.SequenceEnd);
string referenceSeq = utilityObj.xmlUtil.GetTextValue(
Constants.GenBankFileSubSequenceNode, Constants.referenceSeq);
ISequence sequence;
ISequence firstFeatureSeq = null;
// Parse a genBank file.
var refSequence = new Sequence(Alphabets.RNA, referenceSeq);
var parserObj = new GenBankParser();
sequence = parserObj.Parse(filePath).FirstOrDefault();
var metadata =
sequence.Metadata[Constants.GenBank] as GenBankMetadata;
// Get Subsequence feature,start and end postions.
var referenceSequences =
new Dictionary<string, ISequence>();
referenceSequences.Add(Constants.Reference, refSequence);
firstFeatureSeq = metadata.Features.All[0].GetSubSequence(sequence,
referenceSequences);
var sequenceString = new string(firstFeatureSeq.Select(a => (char) a).ToArray());
// Validate SubSequence.
Assert.AreEqual(sequenceString, subSequence);
Assert.AreEqual(metadata.Features.All[0].Location.LocationStart.ToString((IFormatProvider) null),
subSequenceStart);
Assert.AreEqual(metadata.Features.All[0].Location.LocationEnd.ToString((IFormatProvider) null),
subSequenceEnd);
Assert.IsNull(metadata.Features.All[0].Location.Accession);
Assert.AreEqual(metadata.Features.All[0].Location.StartData,
subSequenceStart);
Assert.AreEqual(metadata.Features.All[0].Location.EndData,
subSequenceEnd);
// Log to VSTest GUI
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the Subsequence feature '{0}'",
sequenceString));
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the start of subsequence'{0}'",
metadata.Features.All[0].Location.LocationStart.ToString(
(IFormatProvider) null)));
}
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);
}
/// <summary>
/// Validate GenBank features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Name of the method</param>
private void ValidateGenBankFeatures(string nodeName,
string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string mRNAFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNACount);
string exonFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonCount);
string intronFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronCount);
string cdsFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCount);
string allFeaturesCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GenBankFeaturesCount);
string expectedCDSKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSKey);
string expectedIntronKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronKey);
string expectedExonKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonKey);
string mRNAKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNAKey);
string sourceKeyName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SourceKey);
string proteinKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProteinKeyName);
string tempFileName = Path.GetTempFileName();
ISequenceParser parserObj = new GenBankParser();
IEnumerable<ISequence> sequenceList = parserObj.Parse(filePath);
if (sequenceList.Count() == 1)
{
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq = new Sequence(Utility.GetAlphabet(alphabetName), expectedUpdatedSequence);
orgSeq.ID = sequenceList.ElementAt(0).ID;
orgSeq.Metadata.Add(Constants.GenBank,
sequenceList.ElementAt(0).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
formatterObj.Format(orgSeq, tempFileName);
}
else
{
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq =
new Sequence(Utility.GetAlphabet(alphabetName), expectedUpdatedSequence)
{
ID = sequenceList.ElementAt(1).ID
};
orgSeq.Metadata.Add(Constants.GenBank,
sequenceList.ElementAt(1).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
formatterObj.Format(orgSeq, tempFileName);
}
// parse a temporary file.
var tempParserObj = new GenBankParser();
{
IEnumerable<ISequence> tempFileSeqList = tempParserObj.Parse(tempFileName);
ISequence sequence = tempFileSeqList.ElementAt(0);
var metadata = (GenBankMetadata) sequence.Metadata[Constants.GenBank];
// Validate formatted temporary file GenBank Features.
Assert.AreEqual(metadata.Features.All.Count,
Convert.ToInt32(allFeaturesCount, null));
Assert.AreEqual(metadata.Features.CodingSequences.Count,
Convert.ToInt32(cdsFeatureCount, null));
Assert.AreEqual(metadata.Features.Exons.Count,
Convert.ToInt32(exonFeatureCount, null));
Assert.AreEqual(metadata.Features.Introns.Count,
Convert.ToInt32(intronFeatureCount, null));
Assert.AreEqual(metadata.Features.MessengerRNAs.Count,
Convert.ToInt32(mRNAFeatureCount, null));
Assert.AreEqual(metadata.Features.Attenuators.Count, 0);
Assert.AreEqual(metadata.Features.CAATSignals.Count, 0);
Assert.AreEqual(metadata.Features.DisplacementLoops.Count, 0);
Assert.AreEqual(metadata.Features.Enhancers.Count, 0);
Assert.AreEqual(metadata.Features.Genes.Count, 0);
if ((0 == string.Compare(methodName, "DNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
|| (0 == string.Compare(methodName, "RNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
IList<FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(featureList[0].Key.ToString(null), sourceKeyName);
Assert.AreEqual(featureList[1].Key.ToString(null), mRNAKey);
Assert.AreEqual(featureList[3].Key.ToString(null), expectedCDSKey);
Assert.AreEqual(featureList[5].Key.ToString(null), expectedExonKey);
Assert.AreEqual(featureList[6].Key.ToString(null), expectedIntronKey);
ApplicationLog.WriteLine(
"GenBank Features BVT: Successfully validated the GenBank Features");
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the CDS feature '{0}'",
featureList[3].Key.ToString(null)));
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the Exon feature '{0}'",
featureList[5].Key.ToString(null)));
}
else
{
IList<FeatureItem> proFeatureList = metadata.Features.All;
Assert.AreEqual(proFeatureList[0].Key.ToString(null), sourceKeyName);
Assert.AreEqual(proFeatureList[1].Key.ToString(null), proteinKey);
Assert.AreEqual(proFeatureList[2].Key.ToString(null), expectedCDSKey);
ApplicationLog.WriteLine(
"GenBank Features BVT: Successfully validated the GenBank Features");
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the CDS feature '{0}'",
proFeatureList[2].Key.ToString(null)));
ApplicationLog.WriteLine(string.Format(null,
"GenBank Features BVT: Successfully validated the Source feature '{0}'",
proFeatureList[0].Key.ToString(null)));
}
}
File.Delete(tempFileName);
}
public void TestParsingREFSEQPrimaryHeader()
{
// Test parsing Primary header which contains table with header.
// REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
var results = new GenBankParser()
.Parse(_genBankFile_WithREFSEQPrimaryData)
.ToList();
}
/// <summary>
/// Validate addition of GenBank features.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateAdditionGenBankFeatures(string nodeName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string addFirstKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstKey);
string addSecondKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondKey);
string addFirstLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstLocation);
string addSecondLocation = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondLocation);
string addFirstQualifier = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FirstQualifier);
string addSecondQualifier = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SecondQualifier);
ISequenceParser parser1 = new GenBankParser();
{
IEnumerable<ISequence> seqList1 = parser1.Parse(filePath);
var localBuilderObj = new LocationBuilder();
string tempFileName = Path.GetTempFileName();
string expectedUpdatedSequence =
expectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
var orgSeq = new Sequence(Utility.GetAlphabet(alphabetName),
expectedUpdatedSequence);
orgSeq.ID = seqList1.ElementAt(0).ID;
orgSeq.Metadata.Add(Constants.GenBank,
seqList1.ElementAt(0).Metadata[Constants.GenBank]);
ISequenceFormatter formatterObj = new GenBankFormatter();
{
formatterObj.Format(orgSeq, tempFileName);
// parse GenBank file.
var parserObj = new GenBankParser();
{
IEnumerable<ISequence> seqList = parserObj.Parse(tempFileName);
ISequence seq = seqList.ElementAt(0);
var metadata = (GenBankMetadata) seq.Metadata[Constants.GenBank];
// Add a new features to Genbank features list.
metadata.Features = new SequenceFeatures();
var feature = new FeatureItem(addFirstKey, addFirstLocation);
var qualifierValues = new List<string>();
qualifierValues.Add(addFirstQualifier);
qualifierValues.Add(addFirstQualifier);
feature.Qualifiers.Add(addFirstQualifier, qualifierValues);
metadata.Features.All.Add(feature);
feature = new FeatureItem(addSecondKey, addSecondLocation);
qualifierValues = new List<string>();
qualifierValues.Add(addSecondQualifier);
qualifierValues.Add(addSecondQualifier);
feature.Qualifiers.Add(addSecondQualifier, qualifierValues);
metadata.Features.All.Add(feature);
// Validate added GenBank features.
Assert.AreEqual(metadata.Features.All[0].Key.ToString(null), addFirstKey);
Assert.AreEqual(
localBuilderObj.GetLocationString(metadata.Features.All[0].Location),
addFirstLocation);
Assert.AreEqual(metadata.Features.All[1].Key.ToString(null), addSecondKey);
Assert.AreEqual(localBuilderObj.GetLocationString(metadata.Features.All[1].Location),
addSecondLocation);
parserObj.Close();
}
File.Delete(tempFileName);
}
}
}
/// <summary>
/// Validate GenBank standard features key.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Name of the method</param>
private void ValidateStandardFeaturesKey(string nodeName, string methodName)
{
// Get Values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedCondingSeqCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSCount);
string exonFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExonCount);
string expectedtRNA = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.tRNACount);
string expectedGeneCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.GeneCount);
string miscFeatureCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MiscFeatureCount);
string expectedCDSKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CDSKey);
string expectedIntronKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IntronKey);
string mRNAKey = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.mRNAKey);
string allFeaturesCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StandardFeaturesCount);
// Parse a file.
ISequenceParser parserObj = new GenBankParser();
IEnumerable<ISequence> seq = parserObj.Parse(filePath);
var metadata =
seq.ElementAt(0).Metadata[Constants.GenBank] as GenBankMetadata;
if ((0 == string.Compare(methodName, "DNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
|| (0 == string.Compare(methodName, "RNA",
CultureInfo.CurrentCulture, CompareOptions.IgnoreCase)))
{
// Validate standard features keys.
Assert.AreEqual(metadata.Features.CodingSequences.Count.ToString((IFormatProvider) null),
expectedCondingSeqCount);
Assert.AreEqual(metadata.Features.Exons.Count.ToString((IFormatProvider) null),
exonFeatureCount);
Assert.AreEqual(metadata.Features.TransferRNAs.Count.ToString((IFormatProvider) null),
expectedtRNA);
Assert.AreEqual(metadata.Features.Genes.Count.ToString((IFormatProvider) null),
expectedGeneCount);
Assert.AreEqual(metadata.Features.MiscFeatures.Count.ToString((IFormatProvider) null),
miscFeatureCount);
Assert.AreEqual(StandardFeatureKeys.CodingSequence.ToString(null),
expectedCDSKey);
Assert.AreEqual(StandardFeatureKeys.Intron.ToString(null),
expectedIntronKey);
Assert.AreEqual(StandardFeatureKeys.MessengerRna.ToString(null),
mRNAKey);
Assert.AreEqual(StandardFeatureKeys.All.Count.ToString((IFormatProvider) null),
allFeaturesCount);
}
else
{
Assert.AreEqual(metadata.Features.CodingSequences.Count.ToString((IFormatProvider) null),
expectedCondingSeqCount);
Assert.AreEqual(StandardFeatureKeys.CodingSequence.ToString(null),
expectedCDSKey);
}
}
/// <summary>
/// Validates GenBank Parser for specific test cases
/// which takes ISequenceParser as input.
/// <param name="parser">ISequenceParser object.</param>
/// </summary>
//private static void ValidateParserSpecialTestCases(ISequenceParser parserObj)
private static void ValidateParserSpecialTestCases()
{
ISequenceParser parserObj = new GenBankParser();
{
Assert.IsTrue(File.Exists(FilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format("GenBank Parser : File Exists in the Path '{0}'.",
FilePath));
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 : 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());
}
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(
CultureInfo.CurrentCulture));
}
if (metadata.Locus.DivisionCode != SequenceDivisionCode.None)
{
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
}
Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date);
if (0 != string.Compare(AlphabetName, "rna",
CultureInfo.CurrentCulture,CompareOptions.IgnoreCase))
{
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
}
else
{
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the StrandType, StrandTopology, Division, Date Properties");
}
// Replace all the empty spaces, paragraphs and new line for validation
string updatedExpSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
string updatedActualSequence =
new string(seq.Select(a => (char)a).ToArray()).Replace("\r", "").Replace("\n", "").Replace(" ", "").ToUpper(
CultureInfo.CurrentCulture);
Assert.AreEqual(updatedExpSequence, updatedActualSequence);
ApplicationLog.WriteLine(
"GenBank Parser : Successfully validated the Sequence");
}
}
