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/** Calculate assembly contiguity statistics.
* Written by Shaun Jackman <sjackman@bcgsc.ca>.
*/
#include "config.h"
#include "Common/Histogram.h"
#include "Common/IOUtil.h"
#include "Common/Sequence.h" // for isACGT
#include "Common/Uncompress.h"
#include "DataLayer/FastaReader.h"
#include "DataLayer/Options.h"
#include <algorithm>
#include <getopt.h>
#include <iostream>
#include <sstream>
using namespace std;
#define PROGRAM "abyss-fac"
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]... [FILE]...\n"
"Calculate assembly contiguity statistics.\n"
"\n"
" Options:\n"
"\n"
" -G, -e, --genome-size=N expected genome size. Used to calculate NG50\n"
" and associated stats [disabled]\n"
" -s, -t, --min-length=N ignore sequences shorter than N bp [500]\n"
" -d, --delimiter=S use S for the field delimiter [\\t]\n"
" -j, --jira output JIRA format\n"
" -m, --mmd output MultiMarkdown format\n"
" --chastity discard unchaste sequences [default]\n"
" --no-chastity do not discard unchaste sequences\n"
" --trim-masked trim masked bases from the end\n"
" --no-trim-masked do not trim masked bases from the ends\n"
" of sequences [default]\n"
" --count-ambig count ambiguity codes in sequences\n"
" --no-count-ambig do not count ambiguity codes in sequences [default]\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
"\n"
"Report bugs to <" PACKAGE_BUGREPORT ">.\n";
namespace opt {
static unsigned minLength = 500;
static long long unsigned genomeSize;
static string delimiter = "\t";
static int format;
static int verbose;
static int countAmbig;
}
enum { TAB, JIRA, MMD };
static const char shortopts[] = "d:e:G:jms:t:v";
enum { OPT_HELP = 1, OPT_VERSION };
static const struct option longopts[] = {
{ "genome-size", required_argument, NULL, 'G' },
{ "min-length", no_argument, NULL, 's' },
{ "delimiter", required_argument, NULL, 'd' },
{ "jira", no_argument, NULL, 'j' },
{ "mmd", no_argument, NULL, 'm' },
{ "chastity", no_argument, &opt::chastityFilter, 1 },
{ "no-chastity", no_argument, &opt::chastityFilter, 0 },
{ "trim-masked", no_argument, &opt::trimMasked, 1 },
{ "no-trim-masked", no_argument, &opt::trimMasked, 0 },
{ "count-ambig", no_argument, &opt::countAmbig, 1 },
{ "no-count-ambig", no_argument, &opt::countAmbig, 0 },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
};
/** FastaReader flags. */
static const int FASTAREADER_FLAGS = FastaReader::NO_FOLD_CASE;
/** Print contiguity statistics. */
static void printContiguityStatistics(const char* path)
{
static bool printHeader = true;
if (string(path) == "---") {
if (printHeader == false)
cout << '\n';
printHeader = true;
return;
}
// Read the sequences and count the lengths.
Histogram h;
FastaReader in(path, FASTAREADER_FLAGS);
for (string s; in >> s;)
h.insert(opt::countAmbig ? s.length() :
count_if(s.begin(), s.end(), isACGT));
assert(in.eof());
// Print the table header.
if (opt::format == JIRA && printHeader) {
printHeader = false;
const char* sep = "\t||";
cout << "||"
<< "n" << sep
<< "n:" << opt::minLength << sep
<< "L50" << sep;
if (opt::genomeSize > 0)
cout << "n:NG50" << sep
<< "NG50" << sep;
cout << "min" << sep
<< "N75" << sep
<< "N50" << sep
<< "N25" << sep
<< "E-size" << sep
<< "max" << sep
<< "sum" << sep
<< "name" << sep << '\n';
} else if (opt::format == MMD && printHeader) {
printHeader = false;
const char* sep = "\t|";
cout << "n" << sep
<< "n:" << opt::minLength << sep
<< "L50" << sep;
if (opt::genomeSize > 0)
cout << "n:NG50" << sep
<< "NG50" << sep;
cout << "min" << sep
<< "N75" << sep
<< "N50" << sep
<< "N25" << sep
<< "E-size" << sep
<< "max" << sep
<< "sum" << sep
<< "name" << '\n';
if (opt::genomeSize > 0)
cout << "------" << sep
<< "------" << sep;
cout << "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << sep
<< "------" << '\n';
}
// Print the table.
if (opt::format == JIRA)
cout << '|';
printContiguityStats(cout, h, opt::minLength,
printHeader, opt::delimiter, opt::genomeSize)
<< opt::delimiter << path;
if (opt::format == JIRA)
cout << opt::delimiter;
cout << endl;
printHeader = false;
}
int main(int argc, char** argv)
{
opt::trimMasked = false;
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':
opt::delimiter = arg.str();
arg.clear(ios::eofbit);
break;
case 'j':
opt::delimiter = "\t|";
opt::format = JIRA;
break;
case 'm':
opt::delimiter = "\t|";
opt::format = MMD;
break;
case 'G':
case 'e':
{
double x;
arg >> x;
opt::genomeSize = x;
break;
}
case 's': case 't':
arg >> opt::minLength;
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);
}
if (optind == argc)
printContiguityStatistics("-");
else
for_each(argv + optind, argv + argc,
printContiguityStatistics);
cout.flush();
assert_good(cout, "stdout");
return 0;
}
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