Exemple #1
0
        /// <summary>
        /// For input sequence, constructs k-mers by sliding
        /// a frame of size kmerLength along the input sequence.
        /// Track positions of occurance for each kmer in sequence.
        /// Constructs KmersOfSequence for sequence and associated k-mers.
        /// </summary>
        /// <param name="start">Start index of sequence range.</param>
        /// <param name="end">End index of sequence range.</param>
        /// <param name="kmerLength">Kmer Length.</param>
        /// <param name="sequences">List of sequences.</param>
        /// <returns>Kmer Dictionary.</returns>
        public static Dictionary <string, KmerDataGraphNodePair> BuildPaDeNAKmerDictionary(
            int start,
            int end,
            int kmerLength,
            IList <ISequence> sequences)
        {
            if (kmerLength <= 0)
            {
                throw new ArgumentException(Resource.KmerLengthShouldBePositive);
            }

            if (sequences == null)
            {
                throw new ArgumentNullException("sequences");
            }

            char[] rcBuilder = new char[kmerLength];
            Dictionary <string, KmerDataGraphNodePair> kmerDict = new Dictionary <string, KmerDataGraphNodePair>();

            for (int index = start; index < end; index++)
            {
                // Sequence 'kmer' stores the k-mer in each window.
                // Construct each k-mer using range from sequence
                for (int i = 0; i <= sequences[index].Count - kmerLength; ++i)
                {
                    ISequence kmerSeq = sequences[index].Range(i, kmerLength);
                    if (!kmerSeq.Any <ISequenceItem>(a => a.IsAmbiguous || a.IsGap))
                    {
                        string kmerString          = kmerSeq.ToString();
                        string kmerStringRC        = kmerString.GetReverseComplement(rcBuilder);
                        bool   isNormalOrientation = string.Compare(kmerString, kmerStringRC, StringComparison.OrdinalIgnoreCase) <= 0;
                        string kmer = isNormalOrientation ? kmerString : kmerStringRC; //take the alphabetically first one

                        KmerDataGraphNodePair kmerData;
                        if (!kmerDict.TryGetValue(kmer, out kmerData))
                        {
                            kmerDict.Add(kmer,
                                         new KmerDataGraphNodePair(new KmerData(index, i, isNormalOrientation), isNormalOrientation));
                        }
                        else
                        {
                            kmerData.Kmer.IncrementCount(isNormalOrientation);
                        }
                    }
                }
            }

            return(kmerDict);
        }
Exemple #2
0
 public static ISequence <bool> All <T>(this ISequence <T> source, Func <T, bool> predicate)
 {
     return(source.Any(x => !predicate(x)).Select(x => !x));
 }
Exemple #3
0
 public static ISequence <bool> Any <T>(this ISequence <T> source)
 {
     return(source.Any(x => true));
 }