private static void LoadIndividu(string pIndividu)
{
Console.WriteLine("Informations sur l'individu :" + pIndividu);
log4net.GlobalContext.Properties["iName"] = pIndividu;
cIndividu individu = new cIndividu(pIndividu);
foreach (cSequence item in individu.Sequences)
{
var groupBy = item.Reads.GroupBy(i => i.QNAME);
}
Console.WriteLine("Enregistrement terminé ! (" + individu.Sequences.Count + " sequences)");
}
private static void EnregistreFichier(string fileName, string option)
{
bool isAppend = false;
LogMe("Fichier d'entrée : " + fileName);
switch (option)
{
case "--append":
isAppend = true;
break;
default:
break;
}
//Start Chrono
Stopwatch stopWatch = new Stopwatch();
stopWatch.Start();
LogMe("Traitement du fichier : " + fileName);
cIndividu individu = new cIndividu();
individu.LoadFromFile(fileName);
LogMe("Enregistrement dans la base de données...");
try
{
individu.Save(isAppend);
}
catch (Exception ex)
{
Log.Error("Erreur d'enregistrement de l'individu");
Log.Error(ex);
LogMe("Erreur d'enregistrement de l'individu");
LogMe($"{ex.Message}");
individu.MoveError(fileName);
}
stopWatch.Stop();
// Get the elapsed time as a TimeSpan value.
TimeSpan ts = stopWatch.Elapsed;
// Format and display the TimeSpan value.
string elapsedTime = String.Format("{0:00}:{1:00}:{2:00}.{3:00}",
ts.Hours, ts.Minutes, ts.Seconds,
ts.Milliseconds / 10);
Process proc = Process.GetCurrentProcess();
LogMe("RunTime " + elapsedTime);
LogMe("L'individu '" + individu.Libelle + "' a été enregistré.");
LogMe("Il contient " + individu.Sequences.Count + " séquences.");
LogMe($"EXECTIME;{individu.Libelle};{elapsedTime};{individu.FileLinesCount}");
LogMe($"MEM-PROC;{proc.PrivateMemorySize64.ToString()};{proc.TotalProcessorTime.TotalSeconds.ToString()}");
proc.Dispose();
}
private void genereFile(string individu)
{
cIndividu oIndividu = new cIndividu(individu);
List <string> output = new List <string>();
string idChar = ConfigurationManager.AppSettings["CharIdentificationLigne"];
int unknownAmorces = 0;
LogMe($"Individu chargé");
foreach (cSequence item in oIndividu.Sequences)
{
var reads = item.Reads.GroupBy(i => i.QNAME);
foreach (var read in reads)
{
if (read.Count() != 2)
{
LogMe($"WARNING : Il y a plus de deux reads");
LogMe($"QNAME : {read.Key}");
LogMe($"Sequence : {item.RNAME}");
}
else
{
try
{
foreach (cSequenceRead sequenceRead in read)
{
cAmorceInfo amorceInfo = new cAmorceInfo
{
RNAME = item.RNAME,
FLAG = sequenceRead.FLAG,
POS = sequenceRead.POS
};
sequenceRead.SEQ = amorceInfo.truncateSequence(sequenceRead);
}
var retour = cSequenceRead.ContigeSequence(read.ToList());
var fRead = read.FirstOrDefault();
if (fRead != null)
{
fRead.GestionAmorces(item.RNAME);
output.Add(idChar + read.Key + "|" + fRead.Amorce.NAME);
output.Add(retour);
output.Add(string.Empty);
}
}
catch (ApplicationException ex)
{
unknownAmorces++;
}
catch (Exception ex)
{
LogMe(ex.Message);
}
}
}
}
LogMe($"{unknownAmorces} amorces inconnue(s)");
writeFile(individu, output.ToArray());
}
