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This includes a new amrfinder_index program to re-index the AMRFinderPlus database. It also includes some mostly cosmetic code and error message cleanup and minor updates to github actions.
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| // amrfinder_index.cpp | ||
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| /*=========================================================================== | ||
| * | ||
| * 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 | ||
| * | ||
| */ | ||
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| #ifdef _MSC_VER | ||
| #error "UNIX is required" | ||
| #endif | ||
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| #undef NDEBUG | ||
| #include "common.inc" | ||
| #include "common.hpp" | ||
| using namespace Common_sp; | ||
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| namespace | ||
| { | ||
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| // ThisApplication | ||
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| struct ThisApplication : ShellApplication | ||
| { | ||
| ThisApplication () | ||
| : ShellApplication ("Index the database for AMRFinder", true, true, true) | ||
| { | ||
| addPositional ("DATABASE", "Directory with AMRFinder database"); | ||
| addKey ("blast_bin", "Directory for BLAST ending with '/'", "", '\0', "BLAST_DIR"); | ||
| addFlag ("quiet", "Suppress messages to STDERR", 'q'); | ||
| version = SVN_REV; | ||
| } | ||
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| void shellBody () const final | ||
| { | ||
| const string dbDir = getArg ("DATABASE"); | ||
| const string blast_bin = getArg ("blast_bin"); | ||
| const bool quiet = getFlag ("quiet"); | ||
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| Stderr stderr (quiet); | ||
| stderr << "Running: "<< getCommandLine () << '\n'; | ||
| const Verbose vrb (qc_on); | ||
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| if (! directoryExists (dbDir)) | ||
| throw runtime_error ("Database directory " + dbDir + " does not exist"); | ||
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| const Dir dir (dbDir); | ||
| const string dbDirS (dir. get () + "/"); | ||
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| if (! blast_bin. empty ()) | ||
| prog2dir ["makeblastdb"] = blast_bin; | ||
| findProg ("makeblastdb"); | ||
| findProg ("hmmpress"); | ||
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| // Cf. amrfinder_update.cpp | ||
| StringVector dnaPointMuts; | ||
| { | ||
| LineInput f (dbDirS + "taxgroup.tab"); | ||
| while (f. nextLine ()) | ||
| { | ||
| if (isLeft (f. line, "#")) | ||
| continue; | ||
| string taxgroup, gpipe; | ||
| int n = -1; | ||
| istringstream iss (f. line); | ||
| iss >> taxgroup >> gpipe >> n; | ||
| QC_ASSERT (n >= 0); | ||
| if (n) | ||
| dnaPointMuts << taxgroup; | ||
| } | ||
| } | ||
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| stderr << "Indexing" << "\n"; | ||
| exec (fullProg ("hmmpress") + " -f " + shellQuote (dbDirS + "AMR.LIB") + " > /dev/null 2> " + tmp + "/hmmpress.err", tmp + "/hmmpress.err"); | ||
| setSymlink (dbDirS, tmp + "/db", true); | ||
| exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMRProt" + " -dbtype prot -logfile " + tmp + "/makeblastdb.AMRProt", tmp + "/makeblastdb.AMRProt"); | ||
| exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMR_CDS" + " -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 + " -dbtype nucl -logfile " + tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut, tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut); | ||
| } | ||
| }; | ||
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| } // namespace | ||
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| int main (int argc, | ||
| const char* argv[]) | ||
| { | ||
| ThisApplication app; | ||
| return app. run (argc, argv); | ||
| } | ||
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