From bad67893b4f73eef555c162b77005adca3a3687c Mon Sep 17 00:00:00 2001
From: Aaron Quinlan <aaronquinlan@gmail.com>
Date: Sun, 26 Apr 2009 16:07:34 -0400
Subject: [PATCH] Added linksBed and updated Makefile
---
src/linksBed/Makefile | 44 ++++++++++++
src/linksBed/linksBed.cpp | 134 +++++++++++++++++++++++++++++++++++++
src/linksBed/linksBed.h | 43 ++++++++++++
src/linksBed/linksMain.cpp | 110 ++++++++++++++++++++++++++++++
4 files changed, 331 insertions(+)
create mode 100755 src/linksBed/Makefile
create mode 100755 src/linksBed/linksBed.cpp
create mode 100755 src/linksBed/linksBed.h
create mode 100755 src/linksBed/linksMain.cpp
diff --git a/src/linksBed/Makefile b/src/linksBed/Makefile
new file mode 100755
index 00000000..74856d00
--- /dev/null
+++ b/src/linksBed/Makefile
@@ -0,0 +1,44 @@
+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
diff --git a/src/linksBed/linksBed.cpp b/src/linksBed/linksBed.cpp
new file mode 100755
index 00000000..ad637bb8
--- /dev/null
+++ b/src/linksBed/linksBed.cpp
@@ -0,0 +1,134 @@
+//
+// 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;
+ }
+}
diff --git a/src/linksBed/linksBed.h b/src/linksBed/linksBed.h
new file mode 100755
index 00000000..f104a999
--- /dev/null
+++ b/src/linksBed/linksBed.h
@@ -0,0 +1,43 @@
+#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;
+
+};
diff --git a/src/linksBed/linksMain.cpp b/src/linksBed/linksMain.cpp
new file mode 100755
index 00000000..ce116329
--- /dev/null
+++ b/src/linksBed/linksMain.cpp
@@ -0,0 +1,110 @@
+#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);
+
+}
--
GitLab