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142 lines (105 loc) · 4.44 KB
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// amrfinder_index.cpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Indexing of AMRFinder data
*
* Dependencies: NCBI BLAST, HMMer
*
* Release changes: see amrfinder.cpp
*
*/
#ifdef _MSC_VER
#error "UNIX is required"
#endif
#undef NDEBUG
#include "common.hpp"
using namespace Common_sp;
#include "common.inc"
namespace
{
// ThisApplication
struct ThisApplication final : ShellApplication
{
ThisApplication ()
: ShellApplication ("Index the database for AMRFinder", true, false, true, true)
{
addPositional ("DATABASE", "Directory with AMRFinder database");
addKey ("blast_bin", "Directory for BLAST", "", '\0', "BLAST_DIR");
addKey ("hmmer_bin", "Directory for HMMer", "", '\0', "HMMER_DIR");
version = SVN_REV;
}
void shellBody () const final
{
string dbDir = getArg ("DATABASE");
string blast_bin = getArg ("blast_bin");
string hmmer_bin = getArg ("hmmer_bin");
addDirSlash (dbDir);
addDirSlash (blast_bin);
addDirSlash (hmmer_bin);
const Verbose vrb (qc_on);
if (! directoryExists (dbDir))
throw runtime_error ("Database directory " + dbDir + " does not exist");
if (! blast_bin. empty ())
prog2dir ["makeblastdb"] = blast_bin;
findProg ("makeblastdb");
if (! hmmer_bin. empty ())
prog2dir ["hmmpress"] = hmmer_bin;
findProg ("hmmpress");
// Cf. amrfinder_update.cpp
StringVector dnaPointMuts;
{
LineInput f (dbDir + "taxgroup.tsv", verbose () ? 1 : 0);
while (f. nextLine ())
{
if (isLeft (f. line, "#"))
continue;
string taxgroup = f. line;
const int n = str2<int> (rfindSplit (taxgroup, '\t'));
const string gpipe = rfindSplit (taxgroup, '\t');
QC_ASSERT (n >= 0);
QC_ASSERT (! contains (taxgroup, ' '));
if (n)
dnaPointMuts << taxgroup;
}
}
stderr. section ("Indexing");
exec (fullProg ("hmmpress") + " -f " + shellQuote (dbDir + "AMR.LIB") + " > /dev/null 2> " + tmp + "/hmmpress.err", tmp + "/hmmpress.err");
setSymlink (dbDir, tmp + "/db", true);
exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMRProt.fa" + " -dbtype prot -logfile " + tmp + "/makeblastdb.AMRProt", tmp + "/makeblastdb.AMRProt");
exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMR_CDS.fa" + " -dbtype nucl -logfile " + tmp + "/makeblastdb.AMR_CDS", tmp + "/makeblastdb.AMR_CDS");
for (const string& dnaPointMut : dnaPointMuts)
exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMR_DNA-" + dnaPointMut + ".fa -dbtype nucl -logfile " + tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut, tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut);
}
};
} // namespace
int main (int argc,
const char* argv[])
{
ThisApplication app;
return app. run (argc, argv);
}