1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
|
//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 "runblastsearchworker.h"
#include "../program/globals.h"
#include "../program/settings.h"
#include "blastsearch.h"
#include "../program/memory.h"
RunBlastSearchWorker::RunBlastSearchWorker(QString blastnCommand, QString tblastnCommand, QString parameters) :
m_blastnCommand(blastnCommand), m_tblastnCommand(tblastnCommand), m_parameters(parameters)
{
}
void RunBlastSearchWorker::runBlastSearch()
{
g_blastSearch->m_cancelRunBlastSearch = false;
bool success;
if (g_blastSearch->m_blastQueries.getQueryCount(NUCLEOTIDE) > 0)
{
g_blastSearch->m_blastOutput += runOneBlastSearch(NUCLEOTIDE, &success);
if (!success)
return;
}
if (g_blastSearch->m_blastQueries.getQueryCount(PROTEIN) > 0 && !g_blastSearch->m_cancelRunBlastSearch)
{
g_blastSearch->m_blastOutput += runOneBlastSearch(PROTEIN, &success);
if (!success)
return;
}
if (g_blastSearch->m_cancelRunBlastSearch)
{
m_error = "BLAST search cancelled.";
emit finishedSearch(m_error);
return;
}
//If the code got here, then the search completed successfully.
g_blastSearch->buildHitsFromBlastOutput();
g_blastSearch->findQueryPaths();
g_blastSearch->m_blastQueries.searchOccurred();
m_error = "";
emit finishedSearch(m_error);
}
QString RunBlastSearchWorker::runOneBlastSearch(SequenceType sequenceType, bool * success)
{
QString blastCommand;
QStringList blastCommandArguments = { "-query" };
if (sequenceType == NUCLEOTIDE) {
blastCommand = m_blastnCommand;
blastCommandArguments << g_blastSearch-> m_tempDirectory + "nucl_queries.fasta";
}
else {
blastCommand = m_tblastnCommand;
blastCommandArguments << g_blastSearch-> m_tempDirectory + "prot_queries.fasta";
}
blastCommandArguments << "-db" << (g_blastSearch->m_tempDirectory + "all_nodes.fasta");
blastCommandArguments << "-outfmt" << "6";
blastCommandArguments += m_parameters.split(" ", Qt::SkipEmptyParts);
g_blastSearch->m_blast = new QProcess();
g_blastSearch->m_blast->start(blastCommand, blastCommandArguments);
bool finished = g_blastSearch->m_blast->waitForFinished(-1);
if (g_blastSearch->m_blast->exitCode() != 0 || !finished)
{
if (g_blastSearch->m_cancelRunBlastSearch)
{
m_error = "BLAST search cancelled.";
emit finishedSearch(m_error);
}
else
{
m_error = "There was a problem running the BLAST search";
QString stdErr = g_blastSearch->m_blast->readAllStandardError();
if (stdErr.length() > 0)
m_error += ":\n\n" + stdErr;
else
m_error += ".";
emit finishedSearch(m_error);
}
*success = false;
return "";
}
QString blastOutput = g_blastSearch->m_blast->readAllStandardOutput();
g_blastSearch->m_blast->deleteLater();
g_blastSearch->m_blast = 0;
*success = true;
return blastOutput;
}
|
