private static GeneInfo ParseGeneInfo(string GeneInfoStr)
{
GeneInfo Gene = new GeneInfo();
//Regex R = new Regex(@"\nNAME\s+(.+)\n", RegexOptions.Multiline);
Regex R = new Regex(@"ENTRY\s+(\w+)\s+", RegexOptions.Multiline);
Match M = R.Match(GeneInfoStr);
Gene.GeneName = M.Groups[1].Captures[0].Value;
R = new Regex(@"\nORGANISM\s+((\w+)\s+(.+))\n", RegexOptions.Multiline);
M = R.Match(GeneInfoStr);
Gene.OrganizmAlias = M.Groups[2].Captures[0].Value;
Gene.OrganizmName = M.Groups[3].Captures[0].Value;
// get position: to get chr (plasmid / chromosome)
R = new Regex(@"\nPOSITION\s+((\d:)?(\d+)..(\d+))\n", RegexOptions.Multiline);
M = R.Match(GeneInfoStr);
if (M.Success)
{
if (M.Groups[2].Captures.Count != 0)
{
Gene.Chr = int.Parse(M.Groups[2].Captures[0].Value.Replace(":", ""));
}
else
{
Gene.Chr = 0;
}
Gene.Start = int.Parse(M.Groups[3].Captures[0].Value);
Gene.Stop = int.Parse(M.Groups[4].Captures[0].Value);
}
return(Gene);
}
public static string AddFastaDescription(string Fasta, GeneInfo Info)
{
return(">" + Info.OrganizmAlias + "|" + Info.GeneName + "\n" + Fasta);
}
public static string AddFastaDescription(string Fasta, GeneInfo Info)
{
return ">" + Info.OrganizmAlias + "|" + Info.GeneName + "\n" + Fasta;
}
private static GeneInfo ParseGeneInfo(string GeneInfoStr)
{
GeneInfo Gene = new GeneInfo();
//Regex R = new Regex(@"\nNAME\s+(.+)\n", RegexOptions.Multiline);
Regex R = new Regex(@"ENTRY\s+(\w+)\s+", RegexOptions.Multiline);
Match M = R.Match(GeneInfoStr);
Gene.GeneName = M.Groups[1].Captures[0].Value;
R = new Regex(@"\nORGANISM\s+((\w+)\s+(.+))\n", RegexOptions.Multiline);
M = R.Match(GeneInfoStr);
Gene.OrganizmAlias = M.Groups[2].Captures[0].Value;
Gene.OrganizmName = M.Groups[3].Captures[0].Value;
// get position: to get chr (plasmid / chromosome)
R = new Regex(@"\nPOSITION\s+((\d:)?(\d+)..(\d+))\n", RegexOptions.Multiline);
M = R.Match(GeneInfoStr);
if (M.Success)
{
if (M.Groups[2].Captures.Count != 0)
Gene.Chr = int.Parse(M.Groups[2].Captures[0].Value.Replace(":", ""));
else
Gene.Chr = 0;
Gene.Start = int.Parse(M.Groups[3].Captures[0].Value);
Gene.Stop = int.Parse(M.Groups[4].Captures[0].Value);
}
return Gene;
}
