Skip to content
Snippets Groups Projects
Commit bad67893 authored by Aaron Quinlan's avatar Aaron Quinlan
Browse files

Added linksBed and updated Makefile

parent ad475658
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
src/linksBed/Makefile 0 → 100755
+ 44
− 0
View file @ bad67893
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= linksMain.cpp linksBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= linksBed
LIBS=
all: $(PROGRAM)
.PHONY: all
$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
@echo " * linking $(PROGRAM)"
@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
.PHONY: clean
\ No newline at end of file
src/linksBed/linksBed.cpp 0 → 100755
+ 134
− 0
View file @ bad67893
//
// linksBed.cpp
// BEDTools
//
// Created by Aaron Quinlan Spring 2009.
// Copyright 2009 Aaron Quinlan. All rights reserved.
//
// Summary: Creates HTML or UCSC browser coordinates from a BED file.
//
#include "linksBed.h"
//
// Constructor
//
BedLinks::BedLinks(string &bedFile, string &base, string &org, string &db) {
this->bedFile = bedFile;
this->bed = new BedFile(bedFile);
this->base = base;
this->org = org;
this->db = db;
}
//
// Destructor
//
BedLinks::~BedLinks(void) {
}
void BedLinks::WriteURL(BED &bed, string &base) {
string position = bed.chrom;
std::stringstream posStream;
posStream << ":" << bed.start << "-" << bed.end;
position.append(posStream.str());
cout << "<tr>" << endl;
cout << "\t<td>" << endl;
cout << "\t\t<a href=" << base << position << ">";
cout << bed.chrom << ":" << bed.start << "-" << bed.end;
cout << "</a>" << endl;
cout << "\t</td>" << endl;
if (this->bed->bedType >= 4) {
cout << "\t<td>" << endl;
cout << bed.name << endl;
cout << "\t</td>" << endl;
}
cout << "</tr>" << endl;
}
void BedLinks::LinksBed() {
// construct the html base.
string org = this->org;
string db = this->db;
string base = this->base;
base.append("/cgi-bin/hgTracks?org=");
base.append(org);
base.append("&db=");
base.append(db);
base.append("&position=");
// create the HTML header
cout << "<html>" << endl <<"\t<body>" << endl;
cout << "<title>" << this->bedFile << "</title>" << endl;
// start the table of entries
cout << "<br>Firefox users: Press and hold the \"apple\" or \"alt\" key and click link to open in new tab." << endl;
cout << "<p style=\"font-family:courier\">" << endl;
cout << "<table border=\"0\"" << endl;
// Are we dealing with a BED file or a BED passed via stdin?
// Case 1: Proper BED File.
if ( (this->bedFile != "") && (this->bedFile != "stdin") ) {
// open the BED file for reading
ifstream bed(bedFile.c_str(), ios::in);
if ( !bed ) {
cerr << "Error: The requested bed file (" <<bedFile << ") could not be opened. Exiting!" << endl;
exit (1);
}
string bedLine;
BED bedEntry;
int lineNum = 0;
cout << "<h3>BED Entries from: " << this->bedFile << "</h3>" << endl;
while (getline(bed, bedLine)) {
vector<string> bedFields;
Tokenize(bedLine,bedFields);
lineNum++;
if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
bedEntry.count = 0;
WriteURL(bedEntry, base);
}
}
cout << "</table>" << endl;
cout << "</p>" << endl;
cout << "\t</body>" << endl <<"</html>" << endl;
}
// Case 2: STDIN.
else {
string bedLine;
BED bedEntry;
int lineNum = 0;
cout << "<h3>BED Entries from: stdin </h3>" << endl;
while (getline(cin, bedLine)) {
vector<string> bedFields;
Tokenize(bedLine,bedFields);
lineNum++;
if (this->bed->parseBedLine(bedEntry, bedFields, lineNum)) {
bedEntry.count = 0;
WriteURL(bedEntry, base);
}
}
cout << "</table>" << endl;
cout << "</p>" << endl;
cout << "\t</body>" << endl <<"</html>" << endl;
}
}
src/linksBed/linksBed.h 0 → 100755
+ 43
− 0
View file @ bad67893
#include "bedFile.h"
#include <vector>
#include <algorithm>
#include <map>
#include <list>
#include <iostream>
#include <fstream>
using namespace std;
//***********************************************
// Typedefs
//***********************************************
typedef list<BED> bedList;
//************************************************
// Class methods and elements
//************************************************
class BedLinks {
public:
// constructor
BedLinks(string &, string &, string &, string &);
// destructor
~BedLinks(void);
void WriteURL(BED &, string &);
void LinksBed(); // the default. sorts by chrom (asc.) then by start (asc.)
private:
string bedFile;
string base;
string org;
string db;
// instance of a bed file class.
BedFile *bed;
};
src/linksBed/linksMain.cpp 0 → 100755
+ 110
− 0
View file @ bad67893
#include <iostream>
#include "linksBed.h"
using namespace std;
// define our program name
#define PROGRAM_NAME "linksBed"
// define the version
#define VERSION "1.1.0"
// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
// function declarations
void ShowHelp(void);
int main(int argc, char* argv[]) {
// our configuration variables
bool showHelp = false;
// input files
string bedFile;
bool haveBed = false;
string org = "human";
string db = "hg18";
string base = "http://genome.ucsc.edu";
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) ShowHelp();
// 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("-i", 2, parameterLength)) {
haveBed = true;
bedFile = argv[i + 1];
i++;
}
else if(PARAMETER_CHECK("-base", 5, parameterLength)) {
base = argv[i + 1];
i++;
}
else if(PARAMETER_CHECK("-org", 4, parameterLength)) {
org = argv[i + 1];
i++;
}
else if(PARAMETER_CHECK("-db", 3, parameterLength)) {
db = argv[i + 1];
i++;
}
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// make sure we have both input files
if (!haveBed) {
cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
showHelp = true;
}
if (!showHelp) {
BedLinks *bl = new BedLinks(bedFile, base, org, db);
bl->LinksBed();
return 0;
}
else {
ShowHelp();
}
}
void ShowHelp(void) {
cerr << "===============================================" << endl;
cerr << " " <<PROGRAM_NAME << " v" << VERSION << endl ;
cerr << " Aaron Quinlan, Ph.D. (aaronquinlan@gmail.com) " << endl ;
cerr << " Hall Laboratory, University of Virginia" << endl;
cerr << "===============================================" << endl << endl;
cerr << "Description: Creates HTML links from a BED file." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl;
// cerr << "OPTIONS: " << endl;
// cerr << "\t" << "-sizeA\t\t" << "Sort the BED file by feature size in ascending order. Sorts across all chromosomes." << endl << endl;
// cerr << "\t" << "-sizeD\t\t" << "Sort the BED file by feature size in descending order. Sorts across all chromosomes." << endl << endl;
// cerr << "\t" << "-chrThenSizeA\t" << "Sort the BED file by chrom (ascending), then feature size in ascending order." << endl << endl;
// cerr << "\t" << "-chrThenSizeD\t" << "Sort the BED file by chrom (ascending), then feature size in descending order." << endl << endl;
// cerr << "\t" << "-chrThenScoreA\t" << "Sort the BED file by chrom (ascending), then score in ascending order." << endl << endl;
// cerr << "\t" << "-chrThenScoreD\t" << "Sort the BED file by chrom (ascending), then scor size in descending order." << endl << endl;
//
cerr << "NOTES: " << endl;
cerr << "\t" << "-i stdin\t\t" << "Allows BED file A to be read from stdin. E.g.: cat a.bed | sortBed -i stdin" << endl << endl;
cerr << "\t***Only BED3 - BED6 formats allowed.***"<< endl << endl;
// end the program here
exit(1);
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment