/// <summary>
/// Select nodes with the wanted information
/// </summary>
/// <returns>Returns blast hit object, current element</returns>
private void SelectHit(ref BlastHit hit, XmlReader r, ref string curElement)
{
switch (r.NodeType)
{
case XmlNodeType.Element:
curElement = r.Name;
switch (curElement)
{
case "Hit":
hit = new BlastHit();
break;
}
break;
case XmlNodeType.Text:
if (curElement.StartsWith("Hit_", StringComparison.OrdinalIgnoreCase))
{
ParseHit(curElement, r.Value, hit);
}
else if (curElement.StartsWith("Hsp_", StringComparison.OrdinalIgnoreCase))
{
ParseHsp(curElement, r.Value, hit);
}
break;
}
}
/// <summary>
/// Fills the blast hit object with hit data
/// </summary>
/// <returns>Returns blast hit object</returns>
private void ParseHit(string element, string value, BlastHit curHit)
{
switch (element)
{
case "Hit_num":
break;
case "Hit_id":
break;
case "Hit_def":
curHit.Def = value;
break;
case "Hit_accession":
curHit.Accession = value;
break;
case "Hit_len":
break;
case "Hit_hsps":
break;
default:
throw new FormatException($"Unknown element encountered: {element}");
}
}
/// <summary>
/// Parses the xml returned from blast, only included the bare minimum and takes the first blast result
/// Should take the blast result with the best identity (hsp_identity/hsp
/// </summary>
/// <returns>Returns first blast hit</returns>
public BlastHit ParseBlastXml(Stream blastXml)
{
List <BlastHit> allHits = new List <BlastHit>();
BlastHit hit = null;
try
{
var settings = new XmlReaderSettings {
DtdProcessing = DtdProcessing.Ignore
};
StreamReader sr = null;
try
{
sr = new StreamReader(blastXml);
using (XmlReader r = XmlReader.Create(sr, settings))
{
string curElement = string.Empty;
while (r.Read())
{
SelectHit(ref hit, r, ref curElement);
if (hit?.Accession != null && hit?.Def != null &&
hit?.AlignmentLenght != 0 && hit?.Identity != 0)
{
allHits.Add(hit);
hit = null;
}
}
}
}
finally
{
if (sr != null)
{
sr.Dispose();
}
}
}
catch (Exception e)
{
throw e;
}
allHits.RemoveAll(h => h.Def.Contains("PREDICTED"));
var bestHit = CalculateBestHit(allHits);
return(bestHit);
}
/// <summary>
/// Fills the blast hit object with hsp data
/// </summary>
/// <returns>Returns blast hit object</returns>
private void ParseHsp(string element, string value, BlastHit curHit)
{
switch (element)
{
case "Hsp_num":
break;
case "Hsp_bit-score":
break;
case "Hsp_score":
break;
case "Hsp_evalue":
break;
case "Hsp_query-from":
break;
case "Hsp_query-to":
break;
case "Hsp_hit-from":
break;
case "Hsp_hit-to":
break;
case "Hsp_query-frame":
break;
case "Hsp_hit-frame":
break;
case "Hsp_identity":
curHit.Identity = int.Parse(value);
break;
case "Hsp_positive":
break;
case "Hsp_align-len":
curHit.AlignmentLenght = int.Parse(value);
break;
case "Hsp_density":
break;
case "Hsp_qseq":
break;
case "Hsp_hseq":
break;
case "Hsp_midline":
break;
case "Hsp_pattern-from":
break;
case "Hsp_pattern-to":
break;
case "Hsp_gaps":
break;
default:
throw new FormatException($"Unknown element encountered: {element}");
}
}
