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Fix casing of test filenames.

This commit is contained in:
Mark Smith 2017-09-21 15:30:51 -05:00
Родитель 6871909a4a
Коммит 209a6cd84f
8 изменённых файлов: 30 добавлений и 26 удалений
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4
Tests/Bio.Padena.Tests/PadenaBvtTestCases.cs
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@ -33,7 +33,7 @@ namespace Bio.Padena.Tests
{
#region Global Variables
Utility utilityObj = new Utility(@"TestUtils\PadenaTestData\PadenaTestsConfig.xml");
Utility utilityObj = new Utility(@"TestUtils\PaDeNATestData\PadenaTestsConfig.xml");
#endregion Global Variables
@ -872,7 +872,7 @@ namespace Bio.Padena.Tests
{
#region Global Variables
Utility utilityObj = new Utility(@"TestUtils\PadenaTestData\PadenaTestsConfig.xml");
Utility utilityObj = new Utility(@"TestUtils\PaDeNATestData\PadenaTestsConfig.xml");
#endregion Global Variables

2
Tests/Bio.Padena.Tests/PadenaP1TestCases.cs
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@ -1404,7 +1404,7 @@ namespace Bio.Padena.Tests
{
#region Global Variables
readonly Utility utilityObj = new Utility(@"TestUtils\PadenaTestData\PadenaTestsConfig.xml");
readonly Utility utilityObj = new Utility(@"TestUtils\PaDeNATestData\PadenaTestsConfig.xml");
#endregion Global Variables

2
Tests/Bio.Pamsam.Tests/HierarchicalClusteringSerialTests.cs
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@ -105,7 +105,7 @@ namespace Bio.Pamsam.Tests
//Assert.AreEqual(5, hierarchicalClustering.Nodes[6].RightChildren.ID);
// Test on larger dataset
string filepath = @"TestUtils\FASTA\RV11_BBS_all.afa".TestDir();
string filepath = @"TestUtils\Fasta\RV11_BBS_all.afa".TestDir();
FastAParser parser = new FastAParser();
IList<ISequence> orgSequences = parser.Parse(filepath).ToList();

6
Tests/Bio.Pamsam.Tests/MsaBenchMarkTests.cs
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@ -24,7 +24,7 @@ namespace Bio.Pamsam.Tests
[Test]
public void TestMsaBenchMark()
{
string fileDirectory = @"TestUtils\FASTA\Protein\Balibase\RV911\".TestDir();
string fileDirectory = @"TestUtils\Fasta\Protein\Balibase\RV911\".TestDir();
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
@ -215,7 +215,7 @@ namespace Bio.Pamsam.Tests
List<float> allQ = new List<float>();
List<float> allTC = new List<float>();
string fileDirectory = @"TestUtils\FASTA\Protein\SABmark".TestDir();
string fileDirectory = @"TestUtils\Fasta\Protein\SABmark".TestDir();
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
@ -298,7 +298,7 @@ namespace Bio.Pamsam.Tests
var allQ = new List<float>();
var allTC = new List<float>();
string fileDirectory = @"TestUtils\FASTA\RNA\k10".TestDir();
string fileDirectory = @"TestUtils\Fasta\RNA\k10".TestDir();
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;

4
Tests/Bio.Pamsam.Tests/PAMSAMMultipleSequenceAlignmentTests.cs
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@ -150,7 +150,7 @@ namespace Bio.Pamsam.Tests
[Test]
public void TestMuscleMultipleSequenceAlignmentRunningTime()
{
string filepath = @"TestUtils\FASTA\RunningTime\BOX246.xml.afa".TestDir();
string filepath = @"TestUtils\Fasta\RunningTime\BOX246.xml.afa".TestDir();
// Test on DNA benchmark dataset
FastAParser parser = new FastAParser();
@ -159,7 +159,7 @@ namespace Bio.Pamsam.Tests
List<ISequence> sequences = MsaUtils.UnAlign(orgSequences);
//filepath = @"TestUtils\FASTA\RunningTime\12_raw.afa";
//filepath = @"TestUtils\Fasta\RunningTime\12_raw.afa";
//List<ISequence> sequences = parser.Parse(filepath);
int numberOfSequences = orgSequences.Count;

20
Tests/Bio.Tests/IO/Bed/BEDOperationsTests.cs
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@ -305,7 +305,8 @@ namespace Bio.Tests.IO.Bed
SequenceRangeGrouping refSeqRange = parser.ParseRangeGrouping(refSeqRangefile);
SequenceRangeGrouping querySeqRange = parser.ParseRangeGrouping(querySeqRangefile);
string expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED").TestDir();
const string MinOverlap1 = "Result_Subtract_minoverlap1.bed";
string expectedresultpath = System.IO.Path.Combine (direc, MinOverlap1).TestDir();
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -313,7 +314,8 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED").TestDir();
const string MinOverlap0 = "Result_subtract_minoverlap0.bed";
expectedresultpath = System.IO.Path.Combine (direc, MinOverlap0).TestDir();
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -321,7 +323,7 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED").TestDir();
expectedresultpath = System.IO.Path.Combine (direc, MinOverlap1).TestDir();
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -329,7 +331,7 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED").TestDir();
expectedresultpath = System.IO.Path.Combine (direc, MinOverlap0).TestDir();
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -338,7 +340,7 @@ namespace Bio.Tests.IO.Bed
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1.BED").TestDir();
expectedresultpath = System.IO.Path.Combine (direc, MinOverlap1).TestDir();
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.IntervalsWithNoOverlap, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -346,7 +348,7 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0.BED").TestDir();
expectedresultpath = System.IO.Path.Combine (direc, MinOverlap0).TestDir();
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.IntervalsWithNoOverlap, false);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -354,7 +356,8 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, false);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap0_NOnOverlappingPieces.BED").TestDir();
const string MinNoOverlap0 = "Result_Subtract_minoverlap0_NOnOverlappingPieces.BED";
expectedresultpath = System.IO.Path.Combine (direc, MinNoOverlap0).TestDir();
result = refSeqRange.Subtract(querySeqRange, 0, SubtractOutputType.NonOverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);
@ -362,7 +365,8 @@ namespace Bio.Tests.IO.Bed
resultvalue = ValidateParentSeqRange(result, refSeqRange, querySeqRange, true);
Assert.IsTrue(resultvalue);
expectedresultpath = System.IO.Path.Combine (direc, "Result_Subtract_minoverlap1_NOnOverlappingPieces.BED").TestDir();
const string MinNoOverlap1 = "Result_Subtract_minoverlap1_NOnOverlappingPieces.BED";
expectedresultpath = System.IO.Path.Combine (direc, MinNoOverlap1).TestDir();
result = refSeqRange.Subtract(querySeqRange, 1, SubtractOutputType.NonOverlappingPiecesOfIntervals, true);
formatter.Format(result, resultfilepath);
resultvalue = CompareBEDOutput(resultfilepath, expectedresultpath);

12
Tests/Bio.Tests/IO/FastQ/FastQTests.cs
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@ -25,7 +25,7 @@ namespace Bio.Tests.IO.FastQ
[Category("Priority0")]
public void TestFastQWhenParsingOneOfMany()
{
string filepath = @"TestUtils\FASTQ\SRR002012_5.fastq".TestDir();
string filepath = @"TestUtils\FastQ\SRR002012_5.fastq".TestDir();
// Parse
ISequence seq = new FastQParser().ParseOne(filepath);
@ -52,7 +52,7 @@ namespace Bio.Tests.IO.FastQ
[Category("Priority0")]
public void FastQFormatter()
{
string FilepathOriginal = @"TestUtils\FASTQ\SRR002012_5.fastq".TestDir();
string FilepathOriginal = @"TestUtils\FastQ\SRR002012_5.fastq".TestDir();
Assert.IsTrue(File.Exists(FilepathOriginal));
IList<IQualitativeSequence> seqsOriginal;
@ -77,8 +77,8 @@ namespace Bio.Tests.IO.FastQ
Assert.IsNotNull(seqsNew);
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
int countOriginal = seqsOriginal.Count;
int countNew = seqsNew.Count;
Assert.AreEqual(countOriginal, countNew);
int i;
@ -112,7 +112,7 @@ namespace Bio.Tests.IO.FastQ
[Category("Priority0")]
public void FastQFormatterUsingInterface()
{
string FilepathOriginal = @"TestUtils\FASTQ\SRR002012_5.fastq".TestDir();
string FilepathOriginal = @"TestUtils\FastQ\SRR002012_5.fastq".TestDir();
Assert.IsTrue(File.Exists(FilepathOriginal));
string filepathTmp = Path.GetTempFileName();
@ -161,7 +161,7 @@ namespace Bio.Tests.IO.FastQ
[Category("Priority0")]
public void FastQParserForManyFiles()
{
string Path = @"TestUtils\FASTQ".TestDir();
string Path = @"TestUtils\FastQ".TestDir();
Assert.IsTrue(Directory.Exists(Path));
int count = 0;

6
Tests/TestData/TestUtils/GffTestsConfig.xml
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@ -137,7 +137,7 @@
</SimpleGff>
<!-- This node contains the Gff file information for Protein. -->
<SimpleGffProtein>
<FilePath>TestUtils\simple_gff_protein.GFF</FilePath>
<FilePath>TestUtils\Simple_Gff_Protein.GFF</FilePath>
<ExpectedSequence>MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF</ExpectedSequence>
<ExpectedSequenceCount></ExpectedSequenceCount>
<AlphabetName>Protein</AlphabetName>
@ -1463,7 +1463,7 @@
</MaxSequenceGff>
<!-- This node contains the Gff file information for Large Size File. -->
<LargeSizeGff>
<FilePath>TestUtils\LargeSize.gff</FilePath>
<FilePath>TestUtils\LargeSize.GFF</FilePath>
<NumberOfSequences>1</NumberOfSequences>
<ExpectedSequence></ExpectedSequence>
<ExpectedSequenceCount></ExpectedSequenceCount>
@ -20932,7 +20932,7 @@
</LargeSizeGff>
<!-- This node contains the Gff file information for Medium Size File. -->
<MediumSizeGff>
<FilePath>TestUtils\MediumSize.gff</FilePath>
<FilePath>TestUtils\MediumSize.Gff</FilePath>
<NumberOfSequences>1</NumberOfSequences>
<ExpectedSequence></ExpectedSequence>
<ExpectedSequenceCount></ExpectedSequenceCount>