Exemple #1
0
 public void Write(StreamWriter sw, FastqSequence seq)
 {
     sw.WriteLine("@" + seq.Reference);
     sw.WriteLine(seq.SeqString);
     sw.WriteLine(seq.Strand);
     sw.WriteLine(seq.Score);
 }
Exemple #2
0
 public void Write(StreamWriter sw, FastqSequence seq)
 {
   sw.WriteLine("@" + seq.Reference);
   sw.WriteLine(seq.SeqString);
   sw.WriteLine(seq.Strand);
   sw.WriteLine(seq.Score);
 }
Exemple #3
0
        /// <summary>
        /// Gets the IEnumerable of FastqSequence from the stream being parsed.
        /// </summary>
        /// <param name="sr">Stream to be parsed.</param>
        /// <returns>Returns a FastqSequence.</returns>
        public FastqSequence Parse(TextReader sr)
        {
            while (true)
            {
                string line;
                while ((line = sr.ReadLine()) != null)
                {
                    if (!String.IsNullOrWhiteSpace(line))
                    {
                        break;
                    }
                }

                if (line == null)
                {
                    return(null);
                }

                if (!line.StartsWith("@"))
                {
                    throw new Exception("Unrecognized line, should start with @ for query name: " + line);
                }

                var           refer  = line.Substring(1);
                FastqSequence result = new FastqSequence(refer, null);

                if (!AcceptName(result.Name))
                {
                    sr.ReadLine();
                    sr.ReadLine();
                    sr.ReadLine();
                    Console.WriteLine("ignored " + result.Name);
                    continue;
                }

                result.SeqString = sr.ReadLine();
                result.Strand    = sr.ReadLine().StartsWith("-") ? '-' : '+';
                result.Score     = sr.ReadLine();
                if (result.Score == null)
                {
                    throw new Exception("Unrecognized line, cannot find score line of query: " + refer);
                }

                return(result);
            }
        }
Exemple #4
0
    /// <summary>
    /// Gets the IEnumerable of FastqSequence from the stream being parsed.
    /// </summary>
    /// <param name="sr">Stream to be parsed.</param>
    /// <returns>Returns a FastqSequence.</returns>
    public FastqSequence Parse(TextReader sr)
    {
      while (true)
      {
        string line;
        while ((line = sr.ReadLine()) != null)
        {
          if (!String.IsNullOrWhiteSpace(line))
          {
            break;
          }
        }

        if (line == null)
        {
          return null;
        }

        if (!line.StartsWith("@"))
        {
          throw new Exception("Unrecognized line, should start with @ for query name: " + line);
        }

        var refer = line.Substring(1);
        FastqSequence result = new FastqSequence(refer, null);

        if (!AcceptName(result.Name))
        {
          sr.ReadLine();
          sr.ReadLine();
          sr.ReadLine();
          continue;
        }

        result.SeqString = sr.ReadLine();
        result.Strand = sr.ReadLine().StartsWith("-") ? '-' : '+';
        result.Score = sr.ReadLine();
        if (result.Score == null)
        {
          throw new Exception("Unrecognized line, cannot find score line of query: " + refer);
        }

        return result;
      }
    }