public static void PerformLocalBlast(string querypath, string ncbipath, string localpath, string outputpath,
RunCommand command, BlastType blastType, List<FastaObj> fastaSet, string fastaSetPath, bool inclWaitTime)
{
var lb = new LocalBlaster(ncbipath, localpath, outputpath);
lb.CreateLocalBlastDatabase(command, blastType, fastaSet, fastaSetPath, inclWaitTime);
lb.PerformBlast(querypath, inclWaitTime);
//var bo = Program.localBlaster.PerformBlast(queryPath, true);
}
public void CreateLocalBlastDatabase(RunCommand command, BlastType blastType, List<FastaObj> fastaSet, string fastaSetPath, bool includeWaitTime)
{
this._blastType = blastType;
this._fastaSetPath = fastaSetPath;
if (this._blastType == BlastType.Null)
return;
this.command = command;
//Name for local db
if (this._localDBPath.EndsWith(@"\"))
this._localDBPath += @"\";
var outFilePath = this._localDBPath + @"\~tempLocalBlastDB";
//Check for part of db, if exists, remove to force new db creation
if (File.Exists(outFilePath + ".pin"))
File.Delete(outFilePath + ".pin");
var btype = DBCommands[(int)blastType];
if (fastaSet != null)
{
this._fastaDBSet = fastaSet;
File.Delete(fastaSetPath);
FastaObj.CreateMultiFastaFile(fastaSetPath, fastaSet);
}
var cs = @"makeblastdb -in " + fastaSetPath + " -dbtype " + btype + " -out " + outFilePath;
if (!File.Exists(fastaSetPath))
return;
//Create new Database through c# command line simulator/wrapper. Wait for completion
command.RunCommandLine(cs, this._NCBIBlasteEXEPath);
if (includeWaitTime)
while (command.isRunning)
{ }
}
public void Reduce(RunCommand command, string tempDirectory, string queryPath, Dictionary<ArCOGObj, List<FastaObj>> dict)
{
for (int i = 0; i < dict.Count; i++)
{
List<FastaObj> cl;
dict.TryGetValue(dict.Keys.ToList<ArCOGObj>()[i], out cl);
this.CreateLocalBlastDatabase(command, LocalBlaster.BlastType.Protein,
cl, tempDirectory + @"\tempFastaDB.fa", true);
int w = 0;
var cf = new List<FastaObj>(this.FastaDBSet);
while (w < cf.Count)
{
cf[w].CreateLocalFasta(queryPath);
var tbo = this.PerformBlast(queryPath, true);
this.RemoveDataBaseRedundancy(tbo, .8, false);
w++;
}
continue;
}
}
