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#include "dialign.h"
#include "config.h"
#include "Common/Options.h"
#include "FastaReader.h"
#include "IOUtil.h"
#include "Uncompress.h"
#include "alignGlobal.h"
#include <algorithm>
#include <cassert>
#include <cstdlib>
#include <getopt.h>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>
using namespace std;
#define PROGRAM "abyss-align"
static const char VERSION_MESSAGE[] =
PROGRAM " (" PACKAGE_NAME ") " VERSION "\n"
"Written by Shaun Jackman.\n"
"\n"
"Copyright 2014 Canada's Michael Smith Genome Sciences Centre\n";
static const char USAGE_MESSAGE[] =
"Usage: " PROGRAM " [OPTION]... [FASTA]...\n"
"Align multiple sequences globally using either Needleman-Wunsch\n"
"or DIALIGN-TX. Groups of sequences may be separated using `#.'\n"
"\n"
" Arguments:\n"
"\n"
" FASTA sequences in FASTA format\n"
"\n"
" Options:\n"
"\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
"\n"
" DIALIGN-TX options:\n"
"\n"
" -D, --dialign-d=N dialign debug level, default: 0\n"
" -M, --dialign-m=FILE score matrix, default: dna_matrix.scr\n"
" -P, --dialign-p=FILE diagonal length probability distribution\n"
" default: dna_diag_prob_100_exp_550000\n"
"\n"
"Report bugs to <" PACKAGE_BUGREPORT ">.\n";
namespace opt {
static int dialign_debug;
static string dialign_score;
static string dialign_prob;
}
static const char shortopts[] = "v";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
{ "verbose", no_argument, NULL, 'v' },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ "dialign-d", required_argument, NULL, 'D' },
{ "dialign-m", required_argument, NULL, 'M' },
{ "dialign-p", required_argument, NULL, 'P' },
{ NULL, 0, NULL, 0 }
};
/** Align two sequences using the Needlman-Wunsch algorithm.
*/
static void alignPair(const string& seq0, const string& seq1,
ostream& out)
{
NWAlignment align;
unsigned match = alignGlobal(seq0, seq1, align);
float identity = (float)match / align.size();
out << align << identity << "\n\n";
}
/** Align multiple sequences using DIALIGN-TX. */
static void alignMulti(const vector<string>& seq, ostream& out)
{
unsigned match;
string alignment;
string consensus = dialign(seq, alignment, match);
float identity = (float)match / consensus.size();
out << alignment << consensus << '\n' << identity << "\n\n";
}
/** Align the specified sequences. */
static void align(const vector<string>& seq, ostream& out)
{
switch (seq.size()) {
case 0:
return;
case 1:
out << seq.front() << '\n' << 1 << "\n\n";
return;
case 2:
return alignPair(seq[0], seq[1], out);
default:
return alignMulti(seq, out);
}
}
/** Align multiple sequences. */
static void alignFile(const char* path) {
if (opt::verbose > 0)
cerr << "Aligning `" << path << "'\n";
FastaReader in(path, FastaReader::NO_FOLD_CASE);
for (vector<string> seq; in;) {
seq.clear();
FastaRecord fa;
if (in >> fa)
seq.push_back(fa.seq);
while (in.peek() == '>' && in >> fa)
seq.push_back(fa.seq);
align(seq, cout);
}
assert(in.eof());
}
int main(int argc, char** argv)
{
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
istringstream arg(optarg != NULL ? optarg : "");
switch (c) {
case '?': die = true; break;
case 'D': arg >> opt::dialign_debug; break;
case 'M': arg >> opt::dialign_score; break;
case 'P': arg >> opt::dialign_prob; break;
case 'v': opt::verbose++; break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
if (optarg != NULL && !arg.eof()) {
cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (die) {
cerr << "Try `" << PROGRAM
<< " --help' for more information.\n";
exit(EXIT_FAILURE);
}
// Initialize dialign.
init_parameters();
set_parameters_dna();
para->DEBUG = opt::dialign_debug;
para->SCR_MATRIX_FILE_NAME = (char*)opt::dialign_score.c_str();
para->DIAG_PROB_FILE_NAME = (char*)opt::dialign_prob.c_str();
initDialign();
if (optind < argc)
for_each(&argv[optind], &argv[argc], alignFile);
else
alignFile("-");
return 0;
}
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