Esempio n. 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="sequence">Input sequence.</param>
        /// <param name="kmerLength">K-mer length.</param>
        /// <returns>KmersOfSequence constructed from sequence and associated k-mers.</returns>
        public static KmerPositionDictionary BuildKmerDictionary(ISequence sequence, int kmerLength)
        {
            if (sequence == null)
            {
                throw new ArgumentNullException("sequence");
            }

            if (kmerLength > sequence.Count)
            {
                throw new ArgumentException(Properties.Resource.KmerLengthIsTooLong);
            }

            // kmers maintains the map between k-mer strings to list of positions in sequence.
            KmerPositionDictionary kmers = new KmerPositionDictionary();

            // Sequence 'kmer' stores the k-mer in each window.
            // Construct each k-mer using range from sequence.
            for (long i = 0; i <= sequence.Count - kmerLength; ++i)
            {
                ISequence kmerString = sequence.GetSubSequence(i, kmerLength);
                if (kmers.ContainsKey(kmerString))
                {
                    kmers[kmerString].Add(i);
                }
                else
                {
                    kmers[kmerString] = new List <long>()
                    {
                        i
                    };
                }
            }

            return(kmers);
        }
        /// <summary>
        /// Builds k-mers from a list of given input sequences.
        /// For each sequence in input list, constructs a KmersOfSequence
        /// corresponding to the sequence and associated k-mers.
        /// </summary>
        /// <param name="sequences">List of input sequences.</param>
        /// <param name="kmerLength">K-mer length.</param>
        /// <returns>List of KmersOfSequence instances.</returns>
        public static KmerIndexerDictionary BuildKmerDictionary(IList <ISequence> sequences, int kmerLength)
        {
            if (sequences == null)
            {
                throw new ArgumentNullException("sequences");
            }

            if (kmerLength <= 0)
            {
                throw new ArgumentException(Properties.Resource.KmerLengthShouldBePositive);
            }

            Task <KmerPositionDictionary>[] kmerTasks = new Task <KmerPositionDictionary> [sequences.Count];

            for (int index = 0; index < sequences.Count; index++)
            {
                ISequence localSequence = sequences[index];
                kmerTasks[index] = Task <KmerPositionDictionary> .Factory.StartNew(
                    o => BuildKmerDictionary(localSequence, kmerLength), TaskCreationOptions.None);
            }


            IList <KmerIndexer>           kmerIndex;
            List <KmerPositionDictionary> kmerPositionDictionaries = new List <KmerPositionDictionary>(kmerTasks.Length);

            int totalElements = 0;

            for (int index = 0; index < kmerTasks.Length; index++)
            {
                KmerPositionDictionary kmerPositionDictionary = kmerTasks[index].Result;
                kmerPositionDictionaries.Add(kmerPositionDictionary);
                totalElements += kmerPositionDictionary.Count;
            }

            KmerIndexerDictionary maps = new KmerIndexerDictionary(totalElements);

            for (int index = 0; index < kmerPositionDictionaries.Count; index++)
            {
                foreach (KeyValuePair <ISequence, IList <long> > value in kmerPositionDictionaries[index])
                {
                    if (maps.TryGetValue(value.Key, out kmerIndex) ||
                        maps.TryGetValue(value.Key.GetReverseComplementedSequence(), out kmerIndex))
                    {
                        kmerIndex.Add(new KmerIndexer(index, value.Value));
                    }
                    else
                    {
                        maps.Add(value.Key, new List <KmerIndexer> {
                            new KmerIndexer(index, value.Value)
                        });
                    }
                }
            }

            return(maps);
        }
Esempio n. 3
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="sequence">Input sequence.</param>
        /// <param name="kmerLength">K-mer length.</param>
        /// <returns>KmersOfSequence constructed from sequence and associated k-mers.</returns>
        public static KmerPositionDictionary BuildKmerDictionary(ISequence sequence, int kmerLength)
        {
            if (sequence == null)
            {
                throw new ArgumentNullException("sequence");
            }

            if (kmerLength > sequence.Count)
            {
                throw new ArgumentException(Properties.Resource.KmerLengthIsTooLong);
            }

            // kmers maintains the map between k-mer strings to list of positions in sequence.
            KmerPositionDictionary kmers = new KmerPositionDictionary();

            // Sequence 'kmer' stores the k-mer in each window.
            // Construct each k-mer using range from sequence.
            for (long i = 0; i <= sequence.Count - kmerLength; ++i)
            {
                ISequence kmerString = sequence.GetSubSequence(i, kmerLength);
                if (kmers.ContainsKey(kmerString))
                {
                    kmers[kmerString].Add(i);
                }
                else
                {
                    kmers[kmerString] = new List<long>() { i };
                }
            }

            return kmers;
        }