Multifasta Parser is a new parser for fasta files. basically allows you to extract fasta sequences from multifasta file.

multifasta.cs

/*
to compile:
$gmcs multifasta-parser.cs -out:multifasta-parser

to run:
$mono multifasta-parser [/path/multifasta-file]
*/

using System;
using System.IO;

namespace BioMono.Fasta {

public class CutFasta
{

  // reader for multifasta text file
  StreamReader sr;

  // writer 
  StreamWriter sw;

  // destDir: multifasta output directory
  string destDir; 

// constructor 
public CutFasta()
{
  destDir = "";
}

//method to set multifasta file, no memory used
public void Load(string sourceFile)
{
  destDir = Path.GetDirectoryName(sourceFile);
  sr = File.OpenText(Path.GetFullPath(sourceFile));
}

//method to extract sequences from multifasta file
public void Cut()
{
  string line = "";
  int index = 0;
  int sequenceFastaSegmentCounter = -1; 
  char[] tokens = {'>'};
  string seqName = "";

try {
  do {

    line = sr.ReadLine();
    index = line.IndexOf(tokens[0]);
    if(index != -1) { 
     sequenceFastaSegmentCounter++;
     //seqName = line.Substring((index+1),(line.Length-index));
     seqName = line.Substring((index+1));
     Console.WriteLine("seqName: {0}",seqName);

     index = seqName.IndexOf(' ');

     if(index != -1)
      seqName = seqName.Substring(0,index);

     if(sequenceFastaSegmentCounter > 0)
      sw.Close();

     //string newfastafile = destDir + "/" + sequenceFastaSegmentCounter + ".fasta";
     string newfastafile = destDir + "/" + seqName + ".fasta";
     Console.WriteLine("Creating new fasta file {0}",newfastafile); 
     Console.WriteLine("Short seqName: {0}",seqName);
     sw = File.CreateText(newfastafile);
     sw.WriteLine(line);
}
else
 sw.WriteLine(line);
}
while(line!=null);
}
catch(Exception e) { ; }
sr.Close();
sw.Close();
}
}

// testing main class 
public class testCutFasta
{
 
 public static void Main(string[] args)
 { 
  CutFasta cf = new CutFasta();

  Console.WriteLine("Loading fasta file {0}", args[0]);

  cf.Load(args[0]);

  Console.WriteLine("Extracting from fasta file...");
  
  cf.Cut();
 }
}
}