Add new reads_from tool

tools/tax/CMakeLists.txt

@@ -16,6 +16,10 @@ add_executable(aligns_to src/aligns_to.cpp)
 target_link_libraries(aligns_to PRIVATE ReaderLib ${SYS_LIBRARIES})
 links_and_install_subdir(aligns_to tax)
 
+add_executable(reads_from src/reads_from.cpp)
+target_link_libraries(reads_from PRIVATE ReaderLib ${SYS_LIBRARIES})
+links_and_install_subdir(reads_from tax)
+
 add_executable(dump_kmers src/dump_kmers.cpp)
 target_link_libraries(dump_kmers PRIVATE ReaderLib ${SYS_LIBRARIES})
 links_and_install_subdir(dump_kmers tax)

tools/tax/src/config_reads_from.hpp

@@ -0,0 +1,140 @@
+/*===========================================================================
+*
+* 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.
+*
+* ===========================================================================
+*
+*/
+
+#pragma once
+
+#include <string>
+#include <iostream>
+#include <fstream>
+#include <list>
+#include <stdexcept>
+#include "log.h"
+#include "missing_cpp_features.h"
+
+struct Args
+{
+ using FileList = std::list <std::string>;
+ FileList files;
+ std::string spot_filter_file;
+
+ bool unaligned_only = false;
+ bool hide_counts = false, compact = false;
+
+ int optimization_ultrafast_skip_reader = 0;
+
+ Args(int argc, char const *argv[])
+ {
+ int arg = 1;
+ auto have_arg = [&]() -> bool { return arg < argc; };
+ auto pop_arg = [&]() -> std::string {
+ if (have_arg()) {
+ auto const result = argv[arg];
+ ++arg;
+ return std::string(result);
+ }
+ fail("need more args");
+ };
+ std::string file;
+ auto have_file = false;
+
+ while (have_arg()) {
+ auto const &arg = pop_arg();
+
+ if (arg.empty()) {
+USAGE_ERROR:
+ std::string reason = "unexpected argument: \"" + arg + "\"";
+ fail(reason.c_str());
+ }
+ if (arg.front() == '-') {
+ if (arg == "-unaligned_only")
+ unaligned_only = true;
+ else if (arg == "-spot_filter")
+ spot_filter_file = pop_arg();
+ else if (arg == "-optimization_ultrafast_skip_reader")
+ optimization_ultrafast_skip_reader = std::stoi(pop_arg());
+ else
+ goto USAGE_ERROR;
+ }
+ else if (have_file)
+ goto USAGE_ERROR;
+ else {
+ file = arg;
+ have_file = true;
+ }
+ }
+
+ // exactly one should exist
+ if (!have_file)
+ fail("nothing to process");
+
+ if (ends_with(file, ".list"))
+ files = load_list(file);
+ else
+ files.push_back(file);
+
+ if (files.empty())
+ fail("loaded empty list of files to process");
+ }
+
+ static std::list<std::string> load_list(const std::string &filename)
+ {
+ std::ifstream f(filename);
+ if (f.fail())
+ throw std::runtime_error(std::string("cannot open list file ") + filename);
+
+ std::list<std::string> items;
+
+ while (!f.eof())
+ {
+ std::string s;
+ f >> s; 
+ if (f.fail())
+ break;
+
+ items.push_back(s);
+ }
+
+ return items;
+ }
+
+ static void fail [[noreturn]] (const char* reason = "invalid arguments")
+ {
+ LOG(reason);
+ print_usage();
+ exit(1);
+ }
+
+ static void print_usage()
+ {
+ std::cerr <<
+ "need fasta/accession or file containing list of fasta/accession\n"
+ "examples:\n"
+ " reads_from inputs.list # NB. extension is .list\n"
+ " reads_from chr1.fasta # NB. extension is .fasta, .fa, or .fna\n"
+ " reads_from SRR000001 # not one of the above\n"
+ << std::endl;
+ }
+};

tools/tax/src/reads_from.cpp

@@ -0,0 +1,96 @@
+/*===========================================================================
+ *
+ * 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.
+ *
+ * ===========================================================================
+ *
+ */
+
+#include "config_reads_from.hpp"
+
+#include <iostream>
+#include <chrono>
+#include <thread>
+#include <list>
+
+const std::string VERSION = "0.1";
+
+typedef uint64_t hash_t;
+
+#include "reader.h"
+#include "missing_cpp_features.h"
+
+using namespace std;
+using namespace std::chrono;
+
+static int process(Args::FileList const &files, Reader::Params const &params)
+{
+ auto const before = high_resolution_clock::now();
+ auto const multifile = files.size() > 1;
+
+ for (auto &file : files)
+ {
+ LOG(file);
+
+ try {
+ auto reader = Reader::create(file, params);
+ Reader::Fragment frag;
+
+ while (reader->read(&frag)) {
+ cout << '>' << frag.spotid << '\n' <<
+ frag.bases << '\n';
+ }
+ }
+ catch (std::exception const &e)
+ {
+ LOG(e.what());
+ if (!multifile)
+ throw e;
+ }
+ }
+
+ LOG("total time (sec) " << std::chrono::duration_cast<std::chrono::seconds>( high_resolution_clock::now() - before ).count());
+
+ return 0;
+}
+
+static int process(Args const &args)
+{
+ Reader::Params params;
+
+ params.filter_file = args.spot_filter_file;
+ params.ultrafast_skip_reader = args.optimization_ultrafast_skip_reader;
+ params.unaligned_only = args.unaligned_only;
+
+ return process(args.files, params);
+}
+
+int main(int argc, char const *argv[])
+{
+#ifdef __GLIBCXX__
+ std::set_terminate(__gnu_cxx::__verbose_terminate_handler);
+#endif
+
+ LOG("reads_from version " << VERSION);
+
+ return process(Args(argc, argv));
+}
+