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/*****************************************************************************
nucBedMain.cpp
(c) 2009 - Aaron Quinlan
Hall Laboratory
Department of Biochemistry and Molecular Genetics
University of Virginia
aaronquinlan@gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "nucBed.h"
#include "version.h"
using namespace std;
// define our program name
#define PROGRAM_NAME "bedtools nuc"
// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
// function declarations
void nuc_help(void);
int nuc_main(int argc, char* argv[]) {
// our configuration variables
bool showHelp = false;
// input files
string fastaDbFile;
string bedFile;
string pattern;
// checks for existence of parameters
bool haveFastaDb = false;
bool haveBed = false;
bool printSeq = false;
bool hasPattern = false;
bool forceStrand = false;
bool ignoreCase = false;
bool useFullHeader = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
(PARAMETER_CHECK("--help", 5, parameterLength))) {
showHelp = true;
}
}
if(showHelp) nuc_help();
// do some parsing (all of these parameters require 2 strings)
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
if(PARAMETER_CHECK("-fi", 3, parameterLength)) {
if ((i+1) < argc) {
haveFastaDb = true;
fastaDbFile = argv[i + 1];
i++;
}
}
else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
if ((i+1) < argc) {
haveBed = true;
bedFile = argv[i + 1];
i++;
}
}
else if(PARAMETER_CHECK("-seq", 4, parameterLength)) {
printSeq = true;
}
else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
forceStrand = true;
}
else if(PARAMETER_CHECK("-C", 2, parameterLength)) {
ignoreCase = true;
}
else if(PARAMETER_CHECK("-pattern", 8, parameterLength)) {
if ((i+1) < argc) {
hasPattern = true;
pattern = argv[i + 1];
i++;
}
}
else if(PARAMETER_CHECK("-fullHeader", 11, parameterLength)) {
useFullHeader = true;
}
else {
cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
if (!haveFastaDb || !haveBed) {
showHelp = true;
}
if (!showHelp) {
NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq,
hasPattern, pattern, forceStrand, ignoreCase,
useFullHeader);
delete nuc;
}
else {
nuc_help();
}
return 0;
}
void nuc_help(void) {
cerr << "\nTool: bedtools nuc (aka nucBed)" << endl;
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Profiles the nucleotide content of intervals in a fasta file." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>" << endl << endl;
cerr << "Options: " << endl;
cerr << "\t-fi\tInput FASTA file" << endl << endl;
cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl << endl;
cerr << "\t-s\tProfile the sequence according to strand." << endl << endl;
cerr << "\t-seq\tPrint the extracted sequence" << endl << endl;
cerr << "\t-pattern\tReport the number of times a user-defined sequence" << endl;
cerr << "\t\t\tis observed (case-sensitive)." << endl << endl;
cerr << "\t-C\tIgnore case when matching -pattern. By defaulty, case matters." << endl << endl;
cerr << "\t-fullHeader\tUse full fasta header." << endl;
cerr << "\t\t- By default, only the word before the first space or tab "
<< "is used." << endl << endl;
cerr << "Output format: " << endl;
cerr << "\tThe following information will be reported after each BED entry:" << endl;
cerr << "\t 1) %AT content" << endl;
cerr << "\t 2) %GC content" << endl;
cerr << "\t 3) Number of As observed" << endl;
cerr << "\t 4) Number of Cs observed" << endl;
cerr << "\t 5) Number of Gs observed" << endl;
cerr << "\t 6) Number of Ts observed" << endl;
cerr << "\t 7) Number of Ns observed" << endl;
cerr << "\t 8) Number of other bases observed" << endl;
cerr << "\t 9) The length of the explored sequence/interval." << endl;
cerr << "\t 10) The seq. extracted from the FASTA file. (opt., if -seq is used)" << endl;
cerr << "\t 11) The number of times a user's pattern was observed." << endl;
cerr << "\t (opt., if -pattern is used.)" << endl << endl;
// end the program here
exit(1);
}
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