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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library 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
Lesser General Public License for more details.
============================================================================
$Id: blast_run.h 4714 2009-08-24 13:38:02Z weese@PCPOOL.MI.FU-BERLIN.DE $
==========================================================================*/
#ifndef SEQAN_HEADER_BLAST_RUN_H
#define SEQAN_HEADER_BLAST_RUN_H
//SEQAN_NO_DDDOC: do not generate documentation for this file
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
// Different Blast Program Types
//////////////////////////////////////////////////////////////////////////////
// DNA alignments
// blastn compares a nucleotide query sequence against a nucleotide sequence database
struct TagRunBlastN_;
typedef Tag<TagRunBlastN_> const RunBlastN;
// megablast
struct TagRunMegaBlast_;
typedef Tag<TagRunMegaBlast_> const RunMegaBlast;
//blat
struct TagRunBlat_;
typedef Tag<TagRunBlat_> const RunBlat;
// Protein alignments
// blastp compares an amino acid query sequence against a protein sequence database
struct TagRunBlastP_;
typedef Tag<TagRunBlastP_> const RunBlastP;
// blastx compares a nucleotide query sequence translated in all reading frames against a protein sequence database
struct TagRunBlastX_;
typedef Tag<TagRunBlastX_> const RunBlastX;
// tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
struct TagRunTBlastN_;
typedef Tag<TagRunTBlastN_> const RunTBlastN;
// tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page.
struct TagRunTBlastX_;
typedef Tag<TagRunTBlastX_> const RunTBlastX;
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
// Blast Program Calls
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//blastn
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunBlastN_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "blastall";
blastcall << " -p blastn";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params?
std::cout <<"\n"<< blastcall.str()<<"\n";
system((blastcall.str()).c_str());
}
//run without saving the blast report file (saves temporarily)
template<typename TBlast, typename TBlastReport, typename TString, typename TParamString>
void
run(Tag<TBlast> tag,
TString blast_path,
TString db_path,
TString db_name,
TString query_path,
TString query_name,
TBlastReport & blastObj, //BlastReport<BlastHsp<BlastN,THspInfoSpec>,TStoreSpec,TInfoSpec >
TParamString params = "")
{
SEQAN_CHECKPOINT
#ifdef PLATFORM_WINDOWS
String<char> out_path(blast_path);
String<char> out_path2("D:\\emde\\blast\\bin\\data\\");
#else
String<char> out_path(blast_path);
#endif
String<char> outfile_name = "tempseqanblast.out";
_runBlast(blast_path,db_path,db_name,query_path,query_name,out_path,outfile_name,tag,params);
std::fstream strm;
std::stringstream s;
s <<out_path<< outfile_name;
strm.open((s.str()).c_str(),::std::ios_base::in);
read(strm,blastObj, Blast());
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//megablast
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunMegaBlast_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "megablast";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//blat
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlat(TPath1 blat_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunBlat_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blatcall;
blatcall << blat_path << "blat ";
blatcall << db_path << db_name<<" ";
blatcall << query_path << query_name<<" ";
blatcall << " " << params;
blatcall << " -out=blast " << out_path << outfile_name;
//process params
std::cout << blatcall.str() << "\n";
system((blatcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//blastp
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunBlastP_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "blastall";
blastcall << " -p blastp";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//tblastn
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunTBlastN_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "blastall";
blastcall << " -p tblastn";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//tblastx
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunTBlastX_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "blastall";
blastcall << " -p tblastx";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
//blastx
template<typename TString, typename TPath1, typename TPath, typename TParamString>
void
_runBlast(TPath1 blast_path,
TPath db_path,
TString db_name,
TPath query_path,
TString query_name,
TPath out_path,
TString outfile_name,
Tag<TagRunBlastX_>,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "blastall";
blastcall << " -p blastx";
blastcall << " -d " << db_path << db_name;
blastcall << " -i " << query_path << query_name;
blastcall << " -o " << out_path << outfile_name;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
//////////////////////////////////////////////////////////////////////////////
//formatdb
template<typename TStr,typename TString, typename TParamString>
void
_runFormatDB(TStr blast_path,
TStr db_path,
TString db_file,
TParamString params)
{
SEQAN_CHECKPOINT
std::stringstream blastcall;
blastcall << blast_path << "formatdb ";
blastcall << " -i " <<db_path << db_file;
blastcall << " " << params;
//process params
system((blastcall.str()).c_str());
}
}// namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
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