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 TestGenBankWhenParsingOne()
{
// parse
ISequenceParser parser = new GenBankParser();
ISequence seq = parser.ParseOne(_singleProteinSeqGenBankFilename);
// test the non-metadata properties
Assert.IsTrue(seq.IsReadOnly);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual(MoleculeType.DNA, seq.MoleculeType);
Assert.AreEqual("SCU49845", seq.DisplayID);
Assert.AreEqual("SCU49845", seq.ID);
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata = (GenBankMetadata)seq.Metadata["GenBank"];
Assert.AreEqual(metadata.Locus.Strand, SequenceStrandType.None);
Assert.AreEqual("none", metadata.Locus.StrandTopology.ToString().ToLower());
Assert.AreEqual("PLN", metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse("21-JUN-1999"), metadata.Locus.Date);
Assert.AreEqual("1", metadata.Version.Version);
Assert.AreEqual("1293613", metadata.Version.GINumber);
// test that we're correctly putting all types of metadata in the right places
Assert.AreEqual(1, seq.Metadata.Count);
IList <CitationReference> referenceList = metadata.References;
Assert.AreEqual(3, referenceList.Count);
IList <FeatureItem> featureList = metadata.Features.All;
Assert.AreEqual(6, featureList.Count);
Assert.AreEqual(4, featureList[0].Qualifiers.Count);
Assert.AreEqual(5, featureList[1].Qualifiers.Count);
Assert.AreEqual(1, featureList[2].Qualifiers.Count);
// test the sequence string
string expected = @"GATCCTCCATATACAACGGTATCTCCACCTCAGGTTTAGATCTCAACAACGGAACCATTGCCGACATGAGACAGTTAGGTATCGTCGAGAGTTACAAGCTAAAACGAGCAGTAGTCAGCTCTGCATCTGAAGCCGCTGAAGTTCTACTAAGGGTGGATAACATCATCCGTGCAAGACCAAGAACCGCCAATAGACAACATATGTAACATATTTAGGATATACCTCGAAAATAATAAACCGCCACACTGTCATTATTATAATTAGAAACAGAACGCAAAAATTATCCACTATATAATTCAAAGACGCGAAAAAAAAAGAACAACGCGTCATAGAACTTTTGGCAATTCGCGTCACAAATAAATTTTGGCAACTTATGTTTCCTCTTCGAGCAGTACTCGAGCCCTGTCTCAAGAATGTAATAATACCCATCGTAGGTATGGTTAAAGATAGCATCTCCACAACCTCAAAGCTCCTTGCCGAGAGTCGCCCTCCTTTGTCGAGTAATTTTCACTTTTCATATGAGAACTTATTTTCTTATTCTTTACTCTCACATCCTGTAGTGATTGACACTGCAACAGCCACCATCACTAGAAGAACAGAACAATTACTTAATAGAAAAATTATATCTTCCTCGAAACGATTTCCTGCTTCCAACATCTACGTATATCAAGAAGCATTCACTTACCATGACACAGCTTCAGATTTCATTATTGCTGACAGCTACTATATCACTACTCCATCTAGTAGTGGCCACGCCCTATGAGGCATATCCTATCGGAAAACAATACCCCCCAGTGGCAAGAGTCAATGAATCGTTTACATTTCAAATTTCCAATGATACCTATAAATCGTCTGTAGACAAGACAGCTCAAATAACATACAATTGCTTCGACTTACCGAGCTGGCTTTCGTTTGACTCTAGTTCTAGAACGTTCTCAGGTGAACCTTCTTCTGACTTACTATCTGATGCGAACACCACGTTGTATTTCAATGTAATACTCGAGGGTACGGACTCTGCCGACAGCACGTCTTTGAACAATACATACCAATTTGTTGTTACAAACCGTCCATCCATCTCGCTATCGTCAGATTTCAATCTATTGGCGTTGTTAAAAAACTATGGTTATACTAACGGCAAAAACGCTCTGAAACTAGATCCTAATGAAGTCTTCAACGTGACTTTTGACCGTTCAATGTTCACTAACGAAGAATCCATTGTGTCGTATTACGGACGTTCTCAGTTGTATAATGCGCCGTTACCCAATTGGCTGTTCTTCGATTCTGGCGAGTTGAAGTTTACTGGGACGGCACCGGTGATAAACTCGGCGATTGCTCCAGAAACAAGCTACAGTTTTGTCATCATCGCTACAGACATTGAAGGATTTTCTGCCGTTGAGGTAGAATTCGAATTAGTCATCGGGGCTCACCAGTTAACTACCTCTATTCAAAATAGTTTGATAATCAACGTTACTGACACAGGTAACGTTTCATATGACTTACCTCTAAACTATGTTTATCTCGATGACGATCCTATTTCTTCTGATAAATTGGGTTCTATAAACTTATTGGATGCTCCAGACTGGGTGGCATTAGATAATGCTACCATTTCCGGGTCTGTCCCAGATGAATTACTCGGTAAGAACTCCAATCCTGCCAATTTTTCTGTGTCCATTTATGATACTTATGGTGATGTGATTTATTTCAACTTCGAAGTTGTCTCCACAACGGATTTGTTTGCCATTAGTTCTCTTCCCAATATTAACGCTACAAGGGGTGAATGGTTCTCCTACTATTTTTTGCCTTCTCAGTTTACAGACTACGTGAATACAAACGTTTCATTAGAGTTTACTAATTCAAGCCAAGACCATGACTGGGTGAAATTCCAATCATCTAATTTAACATTAGCTGGAGAAGTGCCCAAGAATTTCGACAAGCTTTCATTAGGTTTGAAAGCGAACCAAGGTTCACAATCTCAAGAGCTATATTTTAACATCATTGGCATGGATTCAAAGATAACTCACTCAAACCACAGTGCGAATGCAACGTCCACAAGAAGTTCTCACCACTCCACCTCAACAAGTTCTTACACATCTTCTACTTACACTGCAAAAATTTCTTCTACCTCCGCTGCTGCTACTTCTTCTGCTCCAGCAGCGCTGCCAGCAGCCAATAAAACTTCATCTCACAATAAAAAAGCAGTAGCAATTGCGTGCGGTGTTGCTATCCCATTAGGCGTTATCCTAGTAGCTCTCATTTGCTTCCTAATATTCTGGAGACGCAGAAGGGAAAATCCAGACGATGAAAACTTACCGCATGCTATTAGTGGACCTGATTTGAATAATCCTGCAAATAAACCAAATCAAGAAAACGCTACACCTTTGAACAACCCCTTTGATGATGATGCTTCCTCGTACGATGATACTTCAATAGCAAGAAGATTGGCTGCTTTGAACACTTTGAAATTGGATAACCACTCTGCCACTGAATCTGATATTTCCAGCGTGGATGAAAAGAGAGATTCTCTATCAGGTATGAATACATACAATGATCAGTTCCAATCCCAAAGTAAAGAAGAATTATTAGCAAAACCCCCAGTACAGCCTCCAGAGAGCCCGTTCTTTGACCCACAGAATAGGTCTTCTTCTGTGTATATGGATAGTGAACCAGCAGTAAATAAATCCTGGCGATATACTGGCAACCTGTCACCAGTCTCTGATATTGTCAGAGACAGTTACGGATCACAAAAAACTGTTGATACAGAAAAACTTTTCGATTTAGAAGCACCAGAGAAGGAAAAACGTACGTCAAGGGATGTCACTATGTCTTCACTGGACCCTTGGAACAGCAATATTAGCCCTTCTCCCGTAAGAAAATCAGTAACACCATCACCATATAACGTAACGAAGCATCGTAACCGCCACTTACAAAATATTCAAGACTCTCAAAGCGGTAAAAACGGAATCACTCCCACAACAATGTCAACTTCATCTTCTGACGATTTTGTTCCGGTTAAAGATGGTGAAAATTTTTGCTGGGTCCATAGCATGGAACCAGACAGAAGACCAAGTAAGAAAAGGTTAGTAGATTTTTCAAATAAGAGTAATGTCAATGTTGGTCAAGTTAAGGACATTCACGGACGCATCCCAGAAATGCTGTGATTATACGCAACGATATTTTGCTTAATTTTATTTTCCTGTTTTATTTTTTATTAGTGGTTTACAGATACCCTATATTTTATTTAGTTTTTATACTTAGAGACATTTAATTTTAATTCCATTCTTCAAATTTCATTTTTGCACTTAAAACAAAGATCCAAAAATGCTCTCGCCCTCTTCATATTGAGAATACACTCCATTCAAAATTTTGTCGTCACCGCTGATTAATTTTTCACTAAACTGATGAATAATCAAAGGCCCCACGTCAGAACCGACTAAAGAAGTGAGTTTTATTTTAGGAGGTTGAAAACCATTATTGTCTGGTAAATTTTCATCTTCTTGACATTTAACCCAGTTTGAATCCCTTTCAATTTCTGCTTTTTCCTCCAAACTATCGACCCTCCTGTTTCTGTCCAACTTATGTCCTAGTTCCAATTCGATCGCATTAATAACTGCTTCAAATGTTATTGTGTCATCGTTGACTTTAGGTAATTTCTCCAAATGCATAATCAAACTATTTAAGGAAGATCGGAATTCGTCGAACACTTCAGTTTCCGTAATGATCTGATCGTCTTTATCCACATGTTGTAATTCACTAAAATCTAAAACGTATTTTTCAATGCATAAATCGTTCTTTTTATTAATAATGCAGATGGAAAATCTGTAAACGTGCGTTAATTTAGAAAGAACATCCAGTATAAGTTCTTCTATATAGTCAATTAAAGCAGGATGCCTATTAATGGGAACGAACTGCGGCAAGTTGAATGACTGGTAAGTAGTGTAGTCGAATGACTGAGGTGGGTATACATTTCTATAAAATAAAATCAAATTAATGTAGCATTTTAAGTATACCCTCAGCCACTTCTCTACCCATCTATTCATAAAGCTGACGCAACGATTACTATTTTTTTTTTCTTCTTGGATCTCAGTCGTCGCAAAAACGTATACCTTCTTTTTCCGACCTTTTTTTTAGCTTTCTGGAAAAGTTTATATTAGTTAAACAGGGTCTAGTCTTAGTGTGAAAGCTAGTGGTTTCGATTGACTGATATTAAGAAAGTGGAAATTAAATTAGTAGTGTAGACGTATATGCATATGTATTTCTCGCCTGTTTATGTTTCTACGTACTTTTGATTTATAGCAAGGGGAAAAGAAATACATACTATTTTTTGGTAAAGGTGAAAGCATAATGTAAAAGCTAGAATAAAATGGACGAAATAAAGAGAGGCTTAGTTCATCTTTTTTCCAAAAAGCACCCAATGATAATAACTAAAATGAAAAGGATTTGCCATCTGTCAGCAACATCAGTTGTGTGAGCAATAATAAAATCATCACCTCCGTTGCCTTTAGCGCGTTTGTCGTTTGTATCTTCCGTAATTTTAGTCTTATCAATGGGAATCATAAATTTTCCAATGAATTAGCAATTTCGTCCAATTCTTTTTGAGCTTCTTCATATTTGCTTTGGAATTCTTCGCACTTCTTTTCCCATTCATCTCTTTCTTCTTCCAAAGCAACGATCCTTCTACCCATTTGCTCAGAGTTCAAATCGGCCTCTTTCAGTTTATCCATTGCTTCCTTCAGTTTGGCTTCACTGTCTTCTAGCTGTTGTTCTAGATCCTGGTTTTTCTTGGTGTAGTTCTCATTATTAGATCTCAAGTTATTGGAGTCTTCAGCCAATTGCTTTGTATCAGACAATTGACTCTCTAACTTCTCCACTTCACTGTCGAGTTGCTCGTTTTTAGCGGACAAAGATTTAATCTCGTTTTCTTTTTCAGTGTTAGATTGCTCTAATTCTTTGAGCTGTTCTCTCAGCTCCTCATATTTTTCTTGCCATGACTCAGATTCTAATTTTAAGCTATTCAATTTCTCTTTGATC";
Assert.AreEqual(expected, seq.ToString());
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleProteinSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
public void TestGenBankWhenUserSetsDnaAlphabet()
{
// set correct alphabet and parse
ISequenceParser parser = new GenBankParser();
parser.Alphabet = Alphabets.DNA;
ISequence seq = parser.ParseOne(_singleDnaSeqGenBankFilename);
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
// format
ISequenceFormatter formatter = new GenBankFormatter();
string actual = formatter.FormatString(seq);
// test the formatting
Assert.AreEqual(_singleDnaSeqGenBankFileExpectedOutput.Replace(" ", ""), actual.Replace(" ", ""));
}
