public static LabeledDNASequence getHighestGCContent(List <LabeledDNASequence> labeledDNAs)
{
double highestThusfar = double.MinValue;
LabeledDNASequence highestSeq = null;
foreach (var DNASeq in labeledDNAs)
{
var score = findGCContent(DNASeq);
if (score > highestThusfar)
{
highestThusfar = score;
highestSeq = DNASeq;
}
}
return(highestSeq);
}
public static List <LabeledDNASequence> loadFASTA(string fileIncludingPath)
{
string text = System.IO.File.ReadAllText(fileIncludingPath);
List <LabeledDNASequence> result = new List <LabeledDNASequence>();
bool done = false;
int charpointer = 0;
while (!done)
{
//find >
//rest of line to CRLF is the label
int labelStart = text.IndexOf('>', charpointer);
if (labelStart == -1)
{
done = true;
continue;
}
int labelEnd = text.IndexOf("\r\n", labelStart, StringComparison.InvariantCulture);
string label = text.Substring(labelStart, (labelEnd - labelStart));
//scan & accumulate to next >(NOT CRLF). This accumulated text is the DNA string
labelEnd = labelEnd + 2; //Scan past CRLF in label
int DNAStart = labelEnd;
int DNAEnd = text.IndexOf('>', labelEnd);
if (DNAEnd == -1)
{
DNAEnd = (text.Length - 1);
done = true;
}
string DNASequence = text.Substring(DNAStart, (DNAEnd - DNAStart));
DNASequence = stripCRLF(DNASequence);
LabeledDNASequence seq = new LabeledDNASequence
{
Label = label,
DNASequence = DNASequence
};
result.Add(seq);
charpointer = DNAEnd;
}
return(result);
}
public static double findGCContent(LabeledDNASequence lds)
{
return(findGCContent(lds.DNASequence));
}
