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//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage is free software: you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation, either version 3 of the License, or
//(at your option) any later version.
//Bandage is distributed in the hope that it will be useful,
//but WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//GNU General Public License for more details.
//You should have received a copy of the GNU General Public License
//along with Bandage. If not, see <http://www.gnu.org/licenses/>.
#include "buildblastdatabaseworker.h"
#include <QProcess>
#include "../program/globals.h"
#include "../program/settings.h"
#include <QFile>
#include <QTextStream>
#include <QMapIterator>
#include "../graph/debruijnnode.h"
#include "../graph/assemblygraph.h"
#include "blastsearch.h"
BuildBlastDatabaseWorker::BuildBlastDatabaseWorker(QString makeblastdbCommand) :
m_makeblastdbCommand(makeblastdbCommand)
{
}
void BuildBlastDatabaseWorker::buildBlastDatabase()
{
g_blastSearch->m_cancelBuildBlastDatabase = false;
QFile file(g_blastSearch->m_tempDirectory + "all_nodes.fasta");
file.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out(&file);
QMapIterator<QString, DeBruijnNode*> i(g_assemblyGraph->m_deBruijnGraphNodes);
while (i.hasNext())
{
if (g_blastSearch->m_cancelBuildBlastDatabase)
{
emit finishedBuild("Build cancelled.");
return;
}
i.next();
DeBruijnNode * node = i.value();
out << node->getFasta(true, false, false);
}
file.close();
// Make sure the graph has sequences to BLAST.
bool atLeastOneSequence = false;
QMapIterator<QString, DeBruijnNode*> j(g_assemblyGraph->m_deBruijnGraphNodes);
while (j.hasNext())
{
j.next();
DeBruijnNode * node = j.value();
if (!node->sequenceIsMissing())
{
atLeastOneSequence = true;
break;
}
}
if (!atLeastOneSequence)
{
m_error = "Cannot build the BLAST database as this graph contains no sequences";
emit finishedBuild(m_error);
return;
}
QStringList makeblastdbArguments = { "-in", g_blastSearch->m_tempDirectory + "all_nodes.fasta", "-dbtype", "nucl" };
g_blastSearch->m_makeblastdb = new QProcess();
g_blastSearch->m_makeblastdb->start(m_makeblastdbCommand, makeblastdbArguments);
bool finished = g_blastSearch->m_makeblastdb->waitForFinished(-1);
if (g_blastSearch->m_makeblastdb->exitCode() != 0 || !finished)
{
m_error = "There was a problem building the BLAST database";
QString stdErr = g_blastSearch->m_makeblastdb->readAllStandardError();
if (stdErr.length() > 0)
m_error += ":\n\n" + stdErr;
else
m_error += ".";
}
else if (g_blastSearch->m_cancelBuildBlastDatabase)
m_error = "Build cancelled.";
else
m_error = "";
emit finishedBuild(m_error);
g_blastSearch->m_makeblastdb->deleteLater();
g_blastSearch->m_makeblastdb = 0;
}
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