public void TestGenBankWhenUserSetsDnaAlphabet() { // set correct alphabet and parse ISequenceParser parser = new GenBankParser(); parser.Alphabet = Alphabets.DNA; ISequence seq = parser.Parse(_singleDnaSeqGenBankFilename).FirstOrDefault(); Assert.AreEqual(Alphabets.DNA, seq.Alphabet); // format ISequenceFormatter formatter = new GenBankFormatter(); formatter.Format(seq, TempGenBankFileName); string actual = string.Empty; using (StreamReader reader = new StreamReader(TempGenBankFileName)) { actual = reader.ReadToEnd(); } File.Delete(TempGenBankFileName); // test the formatting Assert.AreEqual(Utility.CleanupWhiteSpace(_singleDnaSeqGenBankFileExpectedOutput), Utility.CleanupWhiteSpace(actual)); }
public void GenBankFormatterValidateWriteUsingStream() { InitializeXmlVariables(); // Create a Sequence with all attributes. // Parse and update the properties instead of parsing entire file. 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 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(Utility.CleanupWhiteSpace(_singleProteinSeqGenBankFileExpectedOutput), Utility.CleanupWhiteSpace(actual)); }
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext) { GenBankFormatter formatter = new GenBankFormatter(); if ((Sequence == null) && (SequenceList != null)) { formatter.Format(SequenceList, OutputFile); } else if ((Sequence != null) && (SequenceList == null)) { formatter.Format(Sequence, OutputFile); } else if ((Sequence != null) && (SequenceList != null)) { SequenceList.Add(Sequence); formatter.Format(SequenceList, OutputFile); SequenceList.Remove(Sequence); } return(ActivityExecutionStatus.Closed); }
public void GenBankFormatterWithParseValidateWriteFilePath() { InitializeXmlVariables(); // parse ISequenceParser parserObj = new GenBankParser(); { IEnumerable <ISequence> seqList = parserObj.Parse(FilePath); ISequence seq = seqList.ElementAt(0); string tempFileName = Path.GetTempFileName(); ISequenceFormatter formatter = new GenBankFormatter(); { formatter.Format(seq, tempFileName); // parse ISequenceParser parserObjFromFile = new GenBankParser(); seqList = parserObjFromFile.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 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 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 GenBankFormatterValidateReadAndWriteMultipleDBLinks() { // Create a Sequence with all attributes. // parse and update the properties instead of parsing entire file. string tempFileName = Path.GetTempFileName(); ISequenceParser parser1 = new GenBankParser(); using (parser1.Open(_genBankFile_WithMultipleDBLines)) { var orgSeq = parser1.Parse().First(); ISequenceFormatter formatter = new GenBankFormatter(); using (formatter.Open(tempFileName)) { formatter.Format(orgSeq); formatter.Close(); } } var same = Utility.CompareFiles(tempFileName, _genBankFile_WithMultipleDBLines); File.Delete(tempFileName); Assert.IsTrue(same); ApplicationLog.WriteLine("GenBank Formatter: Successful read->write loop"); }
public void GenBankFormatterWithParseValidateFormatFilePath() { InitializeXmlVariables(); // parse ISequenceParser parserObj = new GenBankParser(); IList <ISequence> seqList = parserObj.Parse(FilePath); ISequence seq = seqList[0]; ISequenceFormatter formatter = new GenBankFormatter(); formatter.Format(seq, Constants.GenBankTempFileName); // parse parserObj = new GenBankParser(); seqList = parserObj.Parse(Constants.GenBankTempFileName); seq = seqList[0]; // test the non-metadata properties if (0 == string.Compare(IsSequenceReadOnly, "true", false, CultureInfo.CurrentCulture)) { Assert.IsTrue(seq.IsReadOnly); ApplicationLog.WriteLine("Successfully validated the ReadOnly Property"); } Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet); Assert.AreEqual(Utility.GetMoleculeType(MolType), seq.MoleculeType); Assert.AreEqual(SeqId, seq.DisplayID); Assert.AreEqual(SeqId, seq.ID); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID"); // test the metadata that is tricky to parse, and will not be tested implicitly by // testing the formatting GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"]; if (metadata.Locus.Strand != SequenceStrandType.None) { Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString()); } Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture), metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture)); Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString()); Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date); Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null)); Assert.AreEqual(PrimaryId, metadata.Version.GINumber); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties"); // test the sequence string Assert.AreEqual(ExpectedSequence, seq.ToString()); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the Sequence"); Console.WriteLine(string.Format((IFormatProvider)null, "GenBank Formatter BVT: Successfully validated the Sequence '{0}'", ExpectedSequence)); File.Delete(Constants.GenBankTempFileName); }
public void GenBankFormatterValidateFormatTextWriter() { InitializeXmlVariables(); // Create a Sequence with all attributes. // parse and update the properties instead of parsing entire file. ISequenceParser parser1 = new GenBankParser(); IList <ISequence> seqList1 = parser1.Parse(FilePath); string expectedUpdatedSequence = ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", ""); Sequence orgSeq = new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence); orgSeq.Metadata.Add("GenBank", (GenBankMetadata)seqList1[0].Metadata["GenBank"]); orgSeq.ID = seqList1[0].ID; orgSeq.DisplayID = seqList1[0].DisplayID; orgSeq.MoleculeType = seqList1[0].MoleculeType; ISequenceFormatter formatter = new GenBankFormatter(); using (TextWriter writer = new StreamWriter(Constants.GenBankTempFileName)) { formatter.Format(orgSeq, writer); } // parse GenBankParser parserObj = new GenBankParser(); IList <ISequence> seqList = parserObj.Parse(Constants.GenBankTempFileName); ISequence seq = seqList[0]; // test the non-metadata properties if (0 == string.Compare(IsSequenceReadOnly, "true", false, CultureInfo.CurrentCulture)) { Assert.IsTrue(seq.IsReadOnly); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the ReadOnly Property"); } Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet); Assert.AreEqual(Utility.GetMoleculeType(MolType), seq.MoleculeType); Assert.AreEqual(SeqId, seq.DisplayID); Assert.AreEqual(SeqId, seq.ID); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID"); // test the metadata that is tricky to parse, and will not be tested implicitly by // testing the formatting GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"]; if (metadata.Locus.Strand != SequenceStrandType.None) { Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString()); } Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture), metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture)); Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString()); Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date); Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null)); Assert.AreEqual(PrimaryId, metadata.Version.GINumber); ApplicationLog.WriteLine( "GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties"); // test the sequence string Assert.AreEqual(ExpectedSequence, seq.ToString()); ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence"); Console.WriteLine(string.Format((IFormatProvider)null, "GenBank Formatter BVT: Successfully validated the Sequence '{0}'", ExpectedSequence)); File.Delete(Constants.GenBankTempFileName); }