Пример #1
0
        public void TestGffWhenParsingMultiple()
        {
            // parse
            ISequenceParser parser = new GffParser();
            IEnumerable<ISequence> seqList = parser.Parse(_multipleSeqGffFilename).ToList();

            // test the file-scope metadata that is tricky to parse, and will not be tested
            // implicitly by testing the formatting
            foreach (ISequence seq in seqList)
            {
                var item = seq.Metadata["SOURCE-VERSION"] as MetadataListItem<string>;

                if (item != null)
                {
                    Assert.AreEqual("NCBI", item.SubItems["source"]);
                    Assert.AreEqual("C++", item.SubItems["version"]);
                }

                Assert.AreEqual(DateTime.Parse("2009-10-27", null), seq.Metadata["date"]);
            }

            // just test the formatting; if that's good, the parsing was good
                new GffFormatter()
                .Format(seqList, TempGFFFileName);

            string actual;
            using (StreamReader reader = new StreamReader(TempGFFFileName))
            {
                actual = reader.ReadToEnd();
            }
            
            File.Delete(TempGFFFileName);
            Assert.AreEqual(_multipleSeqGffFileExpectedOutput.Replace("\r\n", Environment.NewLine), actual);
            
        }
Пример #2
0
        public void TestGffForManyFiles()
        {
            // parser and formatter will be used for all files in input dir
            GffFormatter formatter = new GffFormatter();

            // iterate through the files in input dir, parsing and formatting each; write results
            // to log file
            DirectoryInfo inputDirInfo = new DirectoryInfo(_gffDataPath);
            foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gff"))
            {
                ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
                ISequenceParser parser = new GffParser();
                foreach (ISequence 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);
            }
        }
Пример #3
0
        /// <summary>
        /// Parses all test cases related to Parse() method based on the
        /// parameters passed and validates the same.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>        
        void ValidateParseWithStreams(string nodeName)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));

            // Logs information to the log file
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT : File Exists in the Path '{0}'.", filePath));

            IList<ISequence> seqs = null;

            using (var reader = File.OpenRead(filePath))
            {
                GffParser parserObj = new GffParser();
                {
                    seqs = parserObj.Parse(reader).ToList();
                }
            }                                       
            
            int expectedSequenceCount = 1;
            Assert.IsNotNull(seqs);
            Assert.AreEqual(expectedSequenceCount, seqs.Count);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT : Number of Sequences found are '{0}'.",
                seqs.Count.ToString((IFormatProvider)null)));

            Assert.IsTrue(ValidateFeatures(seqs[0], nodeName));
            ApplicationLog.WriteLine(
                "Gff Parser BVT : Successfully validated all the Features for a give Sequence in GFF File.");
            string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.ExpectedSequenceNode);

            Sequence seq = (Sequence)seqs[0];
            Assert.IsNotNull(seq);
            byte[] TempSeqData = new byte[seq.Count];

            for (int i = 0; i < seq.Count; i++)
            {
                TempSeqData[i] = seq[i];
            }
            string sequenceInString = new string(TempSeqData.Select(x => (char)x).ToArray());

            Assert.AreEqual(expectedSequence, sequenceInString);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Gff sequence '{0}' validation after Parse() is found to be as expected.",
                seq.ToString()));

            byte[] tmpEncodedSeq = new byte[seq.Count];

            for (int i = 0; i < seq.Count; i++)
            {
                tmpEncodedSeq[i] = seq[i];
            }

            Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Gff Length sequence '{0}' is as expected.",
                expectedSequence.Length));

            string expectedAlphabet = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture);
            Assert.IsNotNull(seq.Alphabet);
            Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
                expectedAlphabet);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Sequence Alphabet is '{0}' and is as expected.",
                seq.Alphabet.Name));

            string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.SequenceIdNode);
            Assert.AreEqual(expectedSequenceId, seq.ID);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Sequence ID is '{0}' and is as expected.",
                seq.ID));
        }
Пример #4
0
        public void TestGffWhenParsingOne()
        {
            // parse
            GffParser parser = new GffParser();
            ISequence seq = parser.Parse(_singleSeqGffFilename).FirstOrDefault();

            // test the non-metadata properties
            Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
            Assert.AreEqual("NC_001133.7", seq.ID);

            // just test the formatting; if that's good, the parsing was good
            GffFormatter formatter = new GffFormatter();
            string actual = formatter.FormatString(seq);
            Assert.AreEqual(_singleSeqGffFileExpectedOutput.Replace("\r\n", Environment.NewLine), actual);
        }
Пример #5
0
        /// <summary>
        /// Parses all test cases related to ParseOne() method based on the 
        /// parameters passed and validates the same.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>
        /// <param name="isFilePath">Is file path passed as parameter?</param>
        void ValidateParseOneGeneralTestCases(string nodeName, bool isFilePath)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));

            // Logs information to the log file
            ApplicationLog.WriteLine(string.Format("Gff Parser BVT : File Exists in the Path '{0}'.", filePath));

            ISequence originalSeq;
            GffParser parserObj = new GffParser();

            if (isFilePath)
            {
                originalSeq = parserObj.Parse(filePath).First();
            }
            else
            {
                using (var reader = File.OpenRead(filePath))
                {
                    originalSeq = parserObj.Parse(reader).First();
                }
            }

            Assert.IsNotNull(originalSeq);
            Assert.IsTrue(ValidateFeatures(originalSeq, nodeName));
            ApplicationLog.WriteLine(
                "Gff Parser BVT : Successfully validated all the Features for a give Sequence in GFF File.");

            string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);

            string sequenceInString = new string(originalSeq.Select(x => (char)x).ToArray());

            Assert.AreEqual(expectedSequence, sequenceInString);
            ApplicationLog.WriteLine(string.Format("Gff Parser BVT: The Gff sequence '{0}' validation after ParseOne() is found to be as expected.",
                originalSeq.ToString()));

            byte[] tmpEncodedSeq = new byte[originalSeq.Count];
            for (int i = 0; i < originalSeq.Count; i++)
            {
                tmpEncodedSeq[i] = originalSeq[i];
            }
            Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
            ApplicationLog.WriteLine(string.Format("Gff Parser BVT: The Gff Length sequence '{0}' is as expected.",
                expectedSequence.Length));

            string expectedAlphabet = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture);

            Assert.IsNotNull(originalSeq.Alphabet);
            Assert.AreEqual(originalSeq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture), expectedAlphabet);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Sequence Alphabet is '{0}' and is as expected.",
                originalSeq.Alphabet.Name));

            string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.SequenceIdNode);

            Assert.AreEqual(expectedSequenceId, originalSeq.ID);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser BVT: The Sequence ID is '{0}' and is as expected.",
                originalSeq.ID));
        }
Пример #6
0
        /// <summary>
        /// Validates the Format() method in Gff Formatter based on the parameters.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>
        /// <param name="isFilePath">Is file path passed as parameter?</param>
        /// <param name="isSequenceList">Is sequence list passed as parameter?</param>
        void ValidateFormatGeneralTestCases(string nodeName,
            bool isFilePath, bool isSequenceList)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));
            IList<ISequence> seqs = null;
            GffParser parserObj = new GffParser();
            seqs = parserObj.Parse(filePath).ToList();
            Sequence originalSequence = (Sequence)seqs[0];

            // Use the formatter to write the original sequences to a temp file            
            ApplicationLog.WriteLine(string.Format("Gff Formatter BVT: Creating the Temp file '{0}'.",
                Constants.GffTempFileName));

            GffFormatter formatter = new GffFormatter { ShouldWriteSequenceData = true };
            if (isFilePath)
            {
                if (isSequenceList)
                    formatter.Format(seqs, Constants.GffTempFileName);
                else
                    formatter.Format(originalSequence, Constants.GffTempFileName);
            }
            else
            {
                if (isSequenceList)
                {
                    formatter.Format(seqs);
                }
                else
                {
                    formatter.Format(originalSequence);
                }
            }

            // Read the new file, then compare the sequences
            IList<ISequence> seqsNew = null;
            GffParser newParser = new GffParser();
            {
                seqsNew = newParser.Parse(Constants.GffTempFileName).ToList();
            }
            Assert.IsNotNull(seqsNew);
            ApplicationLog.WriteLine(string.Format("Gff Formatter BVT: New Sequence is '{0}'.",
                seqsNew[0].ToString()));

            bool val = ValidateFeatures(seqsNew[0], nodeName);
            Assert.IsTrue(val);
            ApplicationLog.WriteLine(
                "GFF Formatter BVT : All the features validated successfully.");

            // Now compare the sequences.
            int countNew = seqsNew.Count();
            int expectedCount = 1;
            Assert.AreEqual(expectedCount, countNew);
            ApplicationLog.WriteLine("The Number of sequences are matching.");

            Assert.AreEqual(originalSequence.ID, seqsNew[0].ID);          

            string orgSeq = new string(originalSequence.Select(x => (char)x).ToArray()); ; 
            ISequence newSeq = seqsNew.FirstOrDefault();           
            string newSeqString = new string(newSeq.Select(x => (char)x).ToArray());

            Assert.AreEqual(orgSeq, newSeqString);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Formatter BVT: The Gff sequences '{0}' are matching with Format() method.",
                seqsNew[0].ToString()));

            // Passed all the tests, delete the tmp file. If we failed an Assert,
            // the tmp file will still be there in case we need it for debugging.
            if (File.Exists(Constants.GffTempFileName))
                File.Delete(Constants.GffTempFileName);
            ApplicationLog.WriteLine("Deleted the temp file created.");
        }
Пример #7
0
        public void GffFormatterValidateFormatString()
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleGffNodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));
            IList<ISequence> seqs = null;
            GffParser parserObj = new GffParser();
            seqs = parserObj.Parse(filePath).ToList();
            ISequence originalSequence = seqs[0];

            // Use the formatter to write the original sequences to a temp file            
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Formatter BVT: Creating the Temp file '{0}'.", Constants.GffTempFileName));

            GffFormatter formatter = new GffFormatter();
            formatter.ShouldWriteSequenceData = true;
            string formatString = formatter.FormatString(originalSequence);

            string expectedString = utilityObj.xmlUtil.GetTextValue(
                Constants.SimpleGffNodeName, Constants.FormatStringNode);

            expectedString = expectedString.Replace("current-date",
                DateTime.Today.ToString("yyyy-MM-dd", null));
            expectedString =
                expectedString.Replace("\r", "").Replace("\n", "").Replace(" ", "").Replace("\t", "").ToUpper(CultureInfo.CurrentCulture);
            string modifedformatString =
                formatString.Replace("\r", "").Replace("\n", "").Replace(" ", "").Replace("\t", "").ToUpper(CultureInfo.CurrentCulture);

            Assert.AreEqual(modifedformatString, expectedString);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Formatter BVT: The Gff Format String '{0}' are matching with FormatString() method and is as expected.",
                formatString));

            // Passed all the tests, delete the tmp file. If we failed an Assert,
            // the tmp file will still be there in case we need it for debugging.
            File.Delete(Constants.GffTempFileName);
            ApplicationLog.WriteLine("Deleted the temp file created.");
        }
Пример #8
0
 public void GffParserValidateParseWithOneLineFeatures()
 {
     // Gets the expected sequence from the Xml
     string filePath = utilityObj.xmlUtil.GetTextValue(
     Constants.SimpleGffFeaturesNode,
     Constants.FilePathNode);
     Assert.IsTrue(File.Exists(filePath));
     IList<ISequence> seqs = null;
     GffParser parserObj = new GffParser();
     seqs = parserObj.Parse(filePath).ToList();
     Sequence originalSequence = (Sequence)seqs[0];
     bool val = ValidateFeatures(originalSequence,
     Constants.OneLineSeqGffNodeName);
     Assert.IsTrue(val);
     filePath = utilityObj.xmlUtil.GetTextValue(
     Constants.SimpleGffFeaturesReaderNode,
     Constants.FilePathNode);
     GffParser parserObj1 = new GffParser();
     seqs.Add(parserObj1.Parse(filePath).FirstOrDefault());
     originalSequence = (Sequence)seqs[0];
     val = ValidateFeatures(originalSequence,
     Constants.OneLineSeqGffNodeName);
     Assert.IsTrue(val);
     ApplicationLog.WriteLine("GFF Parser BVT : All the features validated successfully.");
 }
Пример #9
0
        /// <summary>
        /// Parses all test cases related to Parse() method with multi sequence 
        /// based on the parameters passed 
        /// and validates the same.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>
        /// <param name="isFilePath">Is file path passed as parameter?</param>
        void ValidateParseMultiSequenceGeneralTestCases(string nodeName,
            bool isFilePath)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));

            // Logs information to the log file
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1 : File Exists in the Path '{0}'.", filePath));

            IList<ISequence> seqs = null;
            GffParser parserObj = new GffParser();

            if (isFilePath)
            {
                seqs = parserObj.Parse(filePath).ToList();
            }
            else
            {
                using (var reader = File.OpenRead(filePath))
                {
                    seqs = parserObj.Parse(reader).ToList();
                }
            }

            int expectedNoOfSeqs = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.NumberOfSequencesNode), null);
            Assert.IsNotNull(seqs);
            Assert.AreEqual(expectedNoOfSeqs, seqs.Count);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1 : Number of Sequences found are '{0}'.",
                seqs.Count.ToString((IFormatProvider)null)));

            string[] expectedSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.ExpectedSequenesNode);
            string[] alphabets = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.AlphabetsNode);
            string[] seqIds = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.SequenceIdsNode);

            for (int i = 0; i < expectedNoOfSeqs; i++)
            {
                bool valFeat = ValidateMultiSequenceFeatures(seqs[i], i + 1, nodeName);

                Assert.IsTrue(valFeat);
                ApplicationLog.WriteLine(
                    "Gff Parser P1 : Successfully validated all the Features for a give Sequence in GFF File.");

                Sequence seq = (Sequence)seqs[i];
                Assert.IsNotNull(seq);                
                string sequenceInString1 = new string(seq.Select(x => (char)x).ToArray());

                if (string.Compare(sequenceInString1, sequenceInString1.ToUpper(CultureInfo.CurrentCulture)) == 0)
                {
                    expectedSequences[i] = expectedSequences[i].ToUpper(CultureInfo.CurrentCulture);
                }
                else
                {
                    expectedSequences[i] = expectedSequences[i].ToLower(CultureInfo.CurrentCulture);
                }
                Assert.AreEqual(expectedSequences[i], sequenceInString1);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Parser P1: The Gff sequence '{0}' validation after Parse() is found to be as expected.",
                    sequenceInString1));

                Assert.AreEqual(expectedSequences[i].Length, sequenceInString1.Length);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Parser P1: The Gff Length sequence '{0}' is as expected.",
                    expectedSequences[i].Length));

                Assert.IsNotNull(seq.Alphabet);
                Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
                    alphabets[i]);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Parser P1: The Sequence Alphabet is '{0}' and is as expected.",
                    seq.Alphabet.Name));

                Assert.AreEqual(seqIds[i], seq.ID);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Parser P1: The Sequence ID is '{0}' and is as expected.", seq.ID));
            }
        }
Пример #10
0
        /// <summary>
        /// Parses all test cases related to Parse() method based on 
        /// the parameters passed and validates the same.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>
        /// <param name="isFilePath">Is file path passed as parameter?</param>
        /// <param name="parseParam">Parse method parameters</param>
        void ValidateParseGeneralTestCases(string nodeName,
            bool isFilePath, ParserParameters parseParam)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));

            // Logs information to the log file
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1 : File Exists in the Path '{0}'.",
                filePath));

            IList<ISequence> seqs = null;
            GffParser parserObj = new GffParser();

            switch (parseParam)
            {
                case ParserParameters.AlphabetProperty:
                    parserObj.Alphabet = Alphabets.DNA;
                    break;
                default:
                    break;
            }

            if (isFilePath)
            {
                seqs = parserObj.Parse(filePath).ToList();
            }
            else
            {
                using (var reader = File.OpenRead(filePath))
                    seqs = parserObj.Parse(reader).ToList();
            }

            Assert.IsNotNull(seqs);
            int expectedCount = 1;
            Assert.AreEqual(expectedCount, seqs.Count);
            ApplicationLog.WriteLine(string.Format("Gff Parser P1 : Number of Sequences found are '{0}'.",
                seqs.Count.ToString((IFormatProvider)null)));

            bool valFeat = ValidateFeatures(seqs[0], nodeName);

            Assert.IsTrue(valFeat);
            ApplicationLog.WriteLine(
                "Gff Parser P1 : Successfully validated all the Features for a give Sequence in GFF File.");

            string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.ExpectedSequenceNode);

            Sequence seq = (Sequence)seqs[0];
            Assert.IsNotNull(seq);                   
            string sequenceInString = new string(seq.Select(x => (char)x).ToArray());

            Assert.AreEqual(expectedSequence, sequenceInString);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,   
                "Gff Parser P1: The Gff sequence '{0}' validation after Parse() is found to be as expected.",
                sequenceInString));

            byte[] TempSeqData1 = new byte[seq.Count];

            for (int i = 0; i < seq.Count; i++)
            {
                TempSeqData1[i] = seq[i];
            }

            Assert.AreEqual(expectedSequence.Length, TempSeqData1.Length);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1: The Gff Length sequence '{0}' is as expected.",
                expectedSequence.Length));

            string expectedAlphabet = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture);

            Assert.IsNotNull(seq.Alphabet);
            Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
                expectedAlphabet);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1: The Sequence Alphabet is '{0}' and is as expected.",
                seq.Alphabet.Name));

            string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.SequenceIdNode);
            Assert.AreEqual(expectedSequenceId, seq.ID);
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Parser P1: The Sequence ID is '{0}' and is as expected.", seq.ID));
        }
Пример #11
0
        /// <summary>
        /// Validates the Format() method in Gff Formatter for Multi sequences based on the parameters.
        /// </summary>
        /// <param name="nodeName">Xml Node name to be read.</param>
        void ValidateFormatMultiSequencesTestCases(string nodeName)
        {
            // Gets the expected sequence from the Xml
            string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.FilePathNode);

            Assert.IsTrue(File.Exists(filePath));
            IList<ISequence> seqs = null;
            GffParser parserObj = new GffParser();
            seqs = parserObj.Parse(filePath).ToList();

            // Use the formatter to write the original sequences to a temp file            
            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                "Gff Formatter P1: Creating the Temp file '{0}'.",
                Constants.GffTempFileName));

            GffFormatter formatter = new GffFormatter { ShouldWriteSequenceData = true };
            formatter.Format(seqs, Constants.GffTempFileName);

            int noOfSeqs = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName,
                Constants.NumberOfSequencesNode), null);
            Assert.IsNotNull(seqs);
            Assert.AreEqual(noOfSeqs, seqs.Count);
            ApplicationLog.WriteLine(string.Format("Gff Formatter P1 : Number of Sequences found are '{0}'.",
                seqs.Count.ToString((IFormatProvider)null)));

            string[] expectedSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.ExpectedSequenesNode);
            string[] alphabets = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.AlphabetsNode);
            string[] seqIds = utilityObj.xmlUtil.GetTextValues(nodeName,
                Constants.SequenceIdsNode);

            for (int i = 0; i < noOfSeqs; i++)
            {
                bool valFeat = ValidateMultiSequenceFeatures(seqs[i], i + 1, nodeName);

                Assert.IsTrue(valFeat);
                ApplicationLog.WriteLine(
                    "Gff Formatter P1 : Successfully validated all the Features for a give Sequence in GFF File.");

                Sequence seq = (Sequence)seqs[i];
                Assert.IsNotNull(seq);

                string newSeq = new string(seq.Select(x => (char)x).ToArray());

                if (string.Compare(newSeq, newSeq.ToUpper(CultureInfo.CurrentCulture)) == 0)
                {
                    expectedSequences[i] = expectedSequences[i].ToUpper(CultureInfo.CurrentCulture);
                }
                else
                {
                    expectedSequences[i] = expectedSequences[i].ToLower(CultureInfo.CurrentCulture);
                }
                Assert.AreEqual(expectedSequences[i], newSeq);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Formatter P1: The Gff sequence '{0}' validation after Parse() is found to be as expected.",
                    newSeq));

                byte[] TempSeqData = new byte[seq.Count];
                for (int j = 0; j < seq.Count; j++)
                {
                    TempSeqData[j] = seq[j];
                }

                Assert.AreEqual(expectedSequences[i].Length, TempSeqData.Length);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Formatter P1: The Gff Length sequence '{0}' is as expected.",
                    expectedSequences[i].Length));

                Assert.IsNotNull(seq.Alphabet);
                Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
                    alphabets[i]);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Formatter P1: The Sequence Alphabet is '{0}' and is as expected.",
                    seq.Alphabet.Name));

                Assert.AreEqual(seqIds[i], seq.ID);
                ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
                    "Gff Formatter P1: The Sequence ID is '{0}' and is as expected.",
                    seq.ID));
            }

            // Passed all the tests, delete the tmp file. If we failed an Assert,
            // the tmp file will still be there in case we need it for debugging.
            if (File.Exists(Constants.GffTempFileName))
                File.Delete(Constants.GffTempFileName);
            ApplicationLog.WriteLine("Deleted the temp file created.");
        }