public GeneCollection FetchGeneData(GeneCollection geneCollection, string[] geneArray, string originSequence)
{
List <string> nonMatchedGenes = new List <string>();
GeneCollection updatedGeneCollection = new GeneCollection();
foreach (String givenGene in geneArray)
{
Boolean isMatch = false;
foreach (Gene gene in geneCollection.collection)
{
if (gene.ID.Contains(givenGene) || gene.LocusTag.Contains(givenGene))
{
int start = gene.StartCoordinate;
int distance = gene.EndCoordinate - gene.StartCoordinate;
string nucleotideSequence = originSequence.Substring(start, distance);
gene.Sequence = nucleotideSequence;
updatedGeneCollection.AddGene(gene);
isMatch = true;
break;
}
}
//If no match was found: add to nonMatchedGenes list.
if (!isMatch)
{
nonMatchedGenes.Add(givenGene);
}
}
//If all or some geneId entries did not match:\
if (nonMatchedGenes.Any())
{
//Display list of gene entries that did not match.
String message = "";
foreach (String gene in nonMatchedGenes)
{
if (message.Length == 0)
{
message += "Some of the provided enrties could not be found. Here is the list of genes; ";
message += gene;
}
else
{
message += ", " + gene;
}
}
Console.WriteLine("\n" + message);
}
updatedGeneCollection.SortOnID();
return(updatedGeneCollection);
}
public CollectedGeneBankData ReadGenebankFile(string inputFile)
{
//Split path to get file name.
GeneCollection geneCollection = new GeneCollection();
CodingSequenceCollection codingSequenceCollection = new CodingSequenceCollection();
string fileName = Path.GetFileName(inputFile);
string organism = "";
string accession = "";
string length = "";
string originSequence = "";
//Booleans for if/else statements.
bool isFirst = true;
bool isOrigin = false;
bool currentEntryIsCDS = false;
bool currentEntryIsGene = false;
//Both patterns check if both complement and non-complement entries are present.
string genePattern = " *gene *(complement)?\\(?\\d*\\.\\.\\d*\\)?";
string cdsPattern = " *CDS *(complement)?\\(?\\d*\\.\\.\\d*\\)?";
string currentEntry = "";
StreamReader reader = new StreamReader(inputFile);
string gbkLine;
while ((gbkLine = reader.ReadLine()) != null)
{
//All comming lines contain nucleotide data which can be added to the origin sequence.
if (isOrigin)
{
originSequence += Regex.Replace(gbkLine, "(\\d| )", "");
}
//Only occurs untill first entry is false.
if (isFirst)
{
if (gbkLine.StartsWith("LOCUS"))
{
length = GetSequenceLength(gbkLine);
}
if (gbkLine.Contains(" ORGANISM"))
{
organism = GetOrganism(gbkLine);
}
if (gbkLine.Contains("ACCESSION"))
{
accession = GetAccessionId(gbkLine);
}
}
//Check if
if (currentEntryIsCDS && !Regex.IsMatch(gbkLine, genePattern))
{
currentEntry += gbkLine + "\n";
}
else if (currentEntryIsCDS && Regex.IsMatch(gbkLine, genePattern))
{
currentEntryIsGene = true;
currentEntryIsCDS = false;
CodingSequence codingSequence = CreateCodingSequenceEntry(currentEntry);
codingSequenceCollection.AddCodingSequence(codingSequence);
currentEntry = gbkLine + "\n";
}
else if (currentEntryIsGene && !Regex.IsMatch(gbkLine, cdsPattern))
{
currentEntry += gbkLine + "\n";
}
else if (currentEntryIsGene && Regex.IsMatch(gbkLine, cdsPattern))
{
currentEntryIsGene = false;
currentEntryIsCDS = true;
Gene gene = CreateGeneEntry(currentEntry);
geneCollection.AddGene(gene);
currentEntry = gbkLine + "\n";
}
else if (isFirst && Regex.IsMatch(gbkLine, genePattern))
{
currentEntryIsGene = true;
isFirst = false;
currentEntry += gbkLine + "\n";
}
else if (isFirst && Regex.IsMatch(gbkLine, cdsPattern))
{
currentEntryIsCDS = true;
isFirst = false;
currentEntry += gbkLine + "\n";
}
if (gbkLine.StartsWith("ORIGIN"))
{
//Set isOrigin to true: first if statement will be handled.
isOrigin = true;
string line = gbkLine.Replace("ORIGIN", "");
originSequence += Regex.Replace(line, "(\\d| )", "");
if (currentEntryIsCDS)
{
currentEntryIsCDS = false;
CodingSequence codingSequence = CreateCodingSequenceEntry(currentEntry);
codingSequenceCollection.AddCodingSequence(codingSequence);
}
else if (currentEntryIsGene)
{
currentEntryIsGene = false;
Gene gene = CreateGeneEntry(currentEntry);
geneCollection.AddGene(gene);
}
}
}
int geneCount = geneCollection.collection.Count; //Size of gene collection
int cdsCount = codingSequenceCollection.collection.Count; //Size of coding sequence collection
double totalGeneCounter = 0.0;
double forwardGeneCounter = 0.0;
foreach (Gene geneEntry in geneCollection.collection)
{
if (!geneEntry.IsReverse)
{
totalGeneCounter++;
forwardGeneCounter++;
}
else
{
totalGeneCounter++;
}
}
//Forward/Reverse (FR) ratio calculation.
double value = (forwardGeneCounter / totalGeneCounter);
double forwardReverseBalance = Math.Round(value, 1);
//For each gene: if gene isForward or !isReverse > +1 to total and foward
//else +1 to total
Summary summary = new Summary(fileName, organism, accession, length, geneCount, forwardReverseBalance, cdsCount, originSequence);
CollectedGeneBankData geneBankeData = new CollectedGeneBankData(geneCollection, codingSequenceCollection, summary);
return(geneBankeData);
}
