Esempio n. 1
0
        private void Create(string RegexFile, string PssmFile, string DatabaseFile, string VariantsFile, string OutputDir, bool grouping)
        {
            string line;

            // regex
            UnixCfg rd = new UnixCfg(RegexFile);

            line = rd.ReadUnixLine();
            if (line == null)
            {
                throw new ApplicationException("Empty regex");
            }
            rd.Close();
            if (PssmFile.Length > 0)
            {
                mRegex = new WregexManager(line, new PSSM(PssmFile), grouping);
            }
            else
            {
                mRegex = new WregexManager(line, grouping);
            }

            // Fasta
            mSeqs = new List <Fasta>();
            if (DatabaseFile.Contains(".fasta"))
            {
                LoadFasta(DatabaseFile);
            }
            else
            {
                SortedList <string, List <Variant> > list = null;
                if (VariantsFile.Length != 0)
                {
                    list = LoadVariants(VariantsFile);
                }
                LoadXml(DatabaseFile, list);
            }

            // Sort Variants
            foreach (Fasta seq in mSeqs)
            {
                seq.mVariants.Sort();
            }

            mDataId    = Path.GetFileNameWithoutExtension(DatabaseFile);
            mOutputDir = OutputDir;
            Directory.CreateDirectory(OutputDir);
        }
Esempio n. 2
0
        private void LoadFasta(string path)
        {
            string line;

            //char[] sep = new char[]{'|',' ','\t'};
            char[]  sep = new char[] { '|' };
            Variant v;
            UnixCfg rd = new UnixCfg(path);

            line = rd.ReadUnixLine();
            if (line == null || line[0] != '>')
            {
                throw new ApplicationException("FASTA header not found");
            }
            Fasta f = new Fasta(Fasta.Type.Protein, line.Split(sep)[0].Substring(1), "");

            do
            {
                line = rd.ReadUnixLine();
                if (line == null || line[0] == '>')             // EOF or next element
                {
                    if (f.mSequence.Length == 0)
                    {
                        throw new ApplicationException("FASTA sequence not found");
                    }
                    mSeqs.Add(f);
                    if (line != null)
                    {
                        f = new Fasta(Fasta.Type.Protein, line.Split(sep)[0].Substring(1), "");
                    }
                }
                else if (line.StartsWith("NP_"))              // Variant
                {
                    v = new Variant(line);
                    if (!f.mVariants.Contains(v))
                    {
                        f.mVariants.Add(v);
                    }
                }
                else         // Sequence
                {
                    f.mSequence += line;
                }
            } while(line != null);
            rd.Close();
        }
Esempio n. 3
0
        /*public void Load( string filename ) {
         *      UnixCfg rd = new UnixCfg( filename );
         *      string line = rd.ReadUnixLine();
         *      char[] sep = new char[]{ ':' };
         *      string[] fields;
         *
         *      while( line != null ) {
         *              PSSMposition pos;
         *              pos.order = uint.Parse( line.Replace("{","") );
         *              pos.entries = new List<PSSMentry>();
         *              line = rd.ReadUnixLine();
         *              while( line != null && !line.Contains("}") ) {
         *                      PSSMentry entry;
         *                      fields = line.Split( sep );
         *                      entry.condition = fields[0].Trim();
         *                      entry.score = double.Parse( fields[1] );
         *                      pos.entries.Add( entry );
         *                      line = rd.ReadUnixLine();
         *              }
         *              if( line != null )
         *                      line = rd.ReadUnixLine();
         *              m_pssm.Add( pos );
         *      }
         *      rd.Close();
         * }*/

        public void Load(string filename)
        {
            UnixCfg rd = new UnixCfg(filename);

            char[]    sep = new char[] { ' ', '\t' };
            string[]  fields;
            PSSMentry entry;

            string line = rd.ReadUnixLine();

            if (line == null)
            {
                rd.Close();
                return;
            }
            fields = line.Split(sep);
            PSSMposition[] pos = new PSSMposition[fields.Length - 1];
            for (uint i = 0; i < pos.Length; i++)
            {
                pos[i].order   = i;
                pos[i].entries = new List <PSSMentry>();
            }
            do
            {
                fields          = line.Split(sep);
                entry.condition = fields[0].Trim();
                for (uint i = 0; i < pos.Length; i++)
                {
                    entry.score = double.Parse(fields[i + 1]);
                    pos[i].entries.Add(entry);
                }
                line = rd.ReadUnixLine();
            } while(line != null);
            rd.Close();

            m_pssm.AddRange(pos);
        }