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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 "reduce.h"
#include "commoncommandlinefunctions.h"
#include "../program/globals.h"
#include "../ui/mygraphicsscene.h"
#include "../ui/mygraphicsview.h"
#include "../graph/assemblygraph.h"
#include <vector>
#include "../program/settings.h"
#include <QPainter>
#include <QSvgGenerator>
#include <QDir>
#include "../blast/blastsearch.h"
int bandageReduce(QStringList arguments)
{
QTextStream out(stdout);
QTextStream err(stderr);
if (checkForHelp(arguments))
{
printReduceUsage(&out, false);
return 0;
}
if (checkForHelpAll(arguments))
{
printReduceUsage(&out, true);
return 0;
}
if (arguments.size() < 2)
{
printReduceUsage(&err, false);
return 1;
}
QString inputFilename = arguments.at(0);
arguments.pop_front();
if (!checkIfFileExists(inputFilename))
{
outputText("Bandage error: " + inputFilename + " does not exist", &err);
return 1;
}
QString outputFilename = arguments.at(0);
arguments.pop_front();
if (!outputFilename.endsWith(".gfa"))
outputFilename += ".gfa";
QString error = checkForInvalidReduceOptions(arguments);
if (error.length() > 0)
{
outputText("Bandage error: " + error, &err);
return 1;
}
bool loadSuccess = g_assemblyGraph->loadGraphFromFile(inputFilename);
if (!loadSuccess)
{
outputText("Bandage error: could not load " + inputFilename, &err);
return 1;
}
parseSettings(arguments);
bool blastUsed = isOptionPresent("--query", &arguments);
if (blastUsed)
{
if (!createBlastTempDirectory())
{
err << "Error creating temporary directory for BLAST files" << Qt::endl;
return 1;
}
QString blastError = g_blastSearch->doAutoBlastSearch();
if (blastError != "")
{
err << blastError << Qt::endl;
return 1;
}
}
QString errorTitle;
QString errorMessage;
std::vector<DeBruijnNode *> startingNodes = g_assemblyGraph->getStartingNodes(&errorTitle, &errorMessage,
g_settings->doubleMode,
g_settings->startingNodes,
"all");
if (errorMessage != "")
{
err << errorMessage << Qt::endl;
return 1;
}
g_assemblyGraph->buildOgdfGraphFromNodesAndEdges(startingNodes, g_settings->nodeDistance);
bool success = g_assemblyGraph->saveVisibleGraphToGfa(outputFilename);
if (!success)
{
err << "Bandage was unable to save the graph file." << Qt::endl;
return 1;
}
deleteBlastTempDirectory();
return 0;
}
void printReduceUsage(QTextStream * out, bool all)
{
QStringList text;
text << "Bandage reduce takes an input graph and saves a reduced subgraph using the graph scope settings. The saved graph will be in GFA format.";
text << "";
text << "If a graph scope is not specified, then the 'entire' scope will be used, in which case this will simply convert the input graph to GFA format.";
text << "";
text << "Usage: Bandage reduce <inputgraph> <outputgraph> [options]";
text << "";
text << "Positional parameters:";
text << "<inputgraph> A graph file of any type supported by Bandage";
text << "<outputgraph> The filename for the GFA graph to be made (if it does not end in '.gfa', that extension will be added)";
text << "";
int nextLineIndex = text.size();
getCommonHelp(&text);
text[nextLineIndex] = "Options: " + text[nextLineIndex];
if (all)
getSettingsUsage(&text);
else
{
nextLineIndex = text.size();
getGraphScopeOptions(&text);
text[nextLineIndex] = "Settings: " + text[nextLineIndex];
}
text << "";
getOnlineHelpMessage(&text);
outputText(text, out);
}
QString checkForInvalidReduceOptions(QStringList arguments)
{
return checkForInvalidOrExcessSettings(&arguments);
}
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