Added expand tool.

Makefile

@@ -29,6 +29,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/clusterBed \
 		  $(SRC_DIR)/complementBed \
 		  $(SRC_DIR)/coverageBed \
+		  $(SRC_DIR)/expand \
 		  $(SRC_DIR)/fastaFromBed \
 		  $(SRC_DIR)/flankBed \
 		  $(SRC_DIR)/genomeCoverageBed \

src/bedtools.cpp

@@ -44,6 +44,7 @@ int closest_main(int argc, char* argv[]); //
 int cluster_main(int argc, char* argv[]); //
 int complement_main(int argc, char* argv[]);//
 int coverage_main(int argc, char* argv[]); //
+int expand_main(int argc, char* argv[]);//
 int fastafrombed_main(int argc, char* argv[]);//
 int flank_main(int argc, char* argv[]); //
 int genomecoverage_main(int argc, char* argv[]);//
@@ -126,6 +127,7 @@ int main(int argc, char *argv[])
     else if (sub_cmd == "links")       return links_main(argc-1, argv+1);
     else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
     else if (sub_cmd == "groupby")     return groupby_main(argc-1, argv+1);
+    else if (sub_cmd == "expand")      return expand_main(argc-1, argv+1);
 
     // help
     else if (sub_cmd == "-h" || sub_cmd == "--help" ||
@@ -225,6 +227,7 @@ int bedtools_help(void)
     cout  << "    links         "  << "Create a HTML page of links to UCSC locations.\n";
     cout  << "    makewindows   "  << "Make interval \"windows\" across a genome.\n";
     cout  << "    groupby       "  << "Group by common cols. & summarize oth. cols. (~ SQL \"groupBy\")\n";
+    cout  << "    expand        "  << "Replicate lines based on lists of values in columns.\n";
 
     cout  << endl;
     cout  << "[ General help ]" << endl;

src/expand/Makefile

+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/tabFile/ \
+           -I$(UTILITIES_DIR)/lineFileUtilities/ \
+           -I$(UTILITIES_DIR)/gzstream/ \
+           -I$(UTILITIES_DIR)/fileType/ \
+           -I$(UTILITIES_DIR)/VectorOps/ \
+           -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= expand.cpp
+OBJECTS= expand.o
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/expand.o
+
+.PHONY: clean

src/expand/expand.cpp

+/*****************************************************************************
+expand.cpp
+
+(c) 2009, 2010, 2011 - Aaron Quinlan
+Center for Public Health Genomics
+University of Virginia
+aaronquinlan@gmail.com
+
+Licenced under the MIT license.
+******************************************************************************/
+#include <vector>
+#include <map>
+#include <numeric>
+#include <algorithm>
+#include <iterator>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <sstream>
+#include <stdlib.h>
+#include <math.h>
+#include <limits.h>
+#include <string.h>
+#include <exception>
+#include <stdexcept> // out_of_range exception
+
+#include "version.h"
+#include "lineFileUtilities.h"
+#include "tabFile.h"
+#include "VectorOps.h"
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "bedtools expand"
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) ((strncmp(argv[i], param, min(actualLen, paramLen))== 0) && \
+                                                              (actualLen == paramLen))
+#define LOOKS_LIKE_A_PARAM(string) (strlen(string)>0 && string[0]=='-')
+
+// function declarations
+void expand_help(void);
+void Expand(const string &inFile, 
+            const vector<int> &expColumns);
+
+int expand_main(int argc, char* argv[]) {
+
+    // input files
+    string inFile             = "stdin";
+    string groupColumnsString = "1,2,3";
+    string expColumnString;
+
+    // our configuration variables
+    bool showHelp          = false;
+    bool haveExpColumns     = 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) expand_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("-i", 2, parameterLength)) {
+            if ((i+1) >= argc || LOOKS_LIKE_A_PARAM(argv[i+1])) {
+                cerr << endl << "*****ERROR: -i parameter requires a value." << endl << endl;
+                expand_help();
+                break;
+            }
+            else {
+                inFile     = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-expcols", 7, parameterLength) || PARAMETER_CHECK("-c", 2, parameterLength)) {
+            if ((i+1) >= argc || LOOKS_LIKE_A_PARAM(argv[i+1])) {
+                cerr << endl << "*****ERROR: -opCols parameter requires a value." << endl << endl;
+                expand_help();
+                break;
+            }
+            else {
+                haveExpColumns       = true;
+                expColumnString     = argv[i + 1];
+                i++;
+            }
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    if (!haveExpColumns) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need -opCols." << endl << "*****" << endl;
+        showHelp = true;
+    }
+    
+
+
+    if (!showHelp) {
+        vector<int> expColumns;
+        Tokenize(expColumnString, expColumns, ',');
+
+        // sanity check the exp columns
+        for(size_t i = 0; i < expColumns.size(); ++i) {
+            int expCol = expColumns[i];
+            if (expCol < 1) {
+                cerr << endl << "*****" << endl << "*****ERROR: expansion columns must be >=1. " << endl << "*****" << endl;
+                expand_help();
+            }
+        }
+        Expand(inFile, expColumns);
+    }
+    else {
+        expand_help();
+    }
+    return 0;
+}
+
+void expand_help(void) {
+
+    cerr << "\nTool:    bedtools expand " << endl;
+    cerr << "Version: " << VERSION << "\n";    
+    cerr << "Summary: Replicate lines in a file based on columns of comma-separated values." << endl << endl;
+
+    cerr << "Usage:\t " << PROGRAM_NAME << " -c [COLS] " << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-i\t"        << "Input file. Assumes \"stdin\" if omitted." << endl << endl;
+
+    cerr << "\t-c \t"    << "Specify the column (1-based) that should be summarized." << endl;
+    cerr                 << "\t\t- Required." << endl;
+
+    cerr << "Examples: " << endl;
+    cerr << "  $ cat test.txt" << endl;
+    cerr << "  chr1	10	20	1,2,3	10,20,30" << endl;
+    cerr << "  chr1	40	50	4,5,6	40,50,60" << endl << endl;
+               
+    cerr << "  $ bedtools expand test.txt -c 5" << endl;
+    cerr << "  chr1	10	20	1,2,3	10" << endl;
+    cerr << "  chr1	10	20	1,2,3	20" << endl;
+    cerr << "  chr1	10	20	1,2,3	30" << endl;
+    cerr << "  chr1	40	50	4,5,6	40" << endl;
+    cerr << "  chr1	40	50	4,5,6	50" << endl;
+    cerr << "  chr1	40	50	4,5,6	60" << endl << endl;
+
+    cerr << "  $ bedtools expand test.txt -c 4,5" << endl;
+    cerr << "  chr1	10	20	1	10" << endl;
+    cerr << "  chr1	10	20	2	20" << endl;
+    cerr << "  chr1	10	20	3	30" << endl;
+    cerr << "  chr1	40	50	4	40" << endl;
+    cerr << "  chr1	40	50	5	50" << endl;
+    cerr << "  chr1	40	50	6	60" << endl;
+
+    // end the program here
+    exit(1);
+
+}
+
+
+void Expand (const string &inFile,
+    const vector<int> &expColumns) 
+{
+
+    // current line number
+    int lineNum = 0;
+    // string representing current line
+    string inLine;
+
+    // vector of strings holding the tokenized current line
+    vector<string>  inFields;
+    inFields.reserve(20);
+
+    // build a map of the columns to be expanded
+    // to allow quic lookups to test if a column is
+    // "normal" or whether it is one of the columns 
+    // that is being expaded
+    map<int, bool> expColMap;
+    for (size_t c = 0; c < expColumns.size(); c++)
+        expColMap[expColumns[c]] = true;
+    
+    // open a new tab file, loop through it line by line
+    // and expand each line into multiple lines according to the
+    // columns the user has requested.
+    // 
+    TabLineStatus tabLineStatus;
+    TabFile *_tab = new TabFile(inFile);
+    _tab->Open();
+    while ((tabLineStatus = _tab->GetNextTabLine(inFields, lineNum)) != TAB_INVALID) {
+        lineNum++;
+        if (tabLineStatus == TAB_VALID) {
+            
+            // a list containing the expanded values (inner) for each column (outer)
+            vector< vector<string> >  expandedCols;
+            
+            // expand each requested column into a vector
+            int prev_size = -1;
+            for (size_t c = 0; c < expColumns.size(); c++)
+            {
+                vector<string> expansion;
+                if ((expColumns[c]-1) >= (int) inFields.size()) {
+                    cerr << endl
+                    << "*****" << endl
+                    << "*****ERROR: Requested column number exceeds number of columns." << endl
+                    << "*****       This was violated at line: " << lineNum << endl
+                    << "*****" << endl;
+                    exit(1);
+                }
+                // expand the requested column into a vector
+                Tokenize(inFields[expColumns[c]-1], expansion, ',');
+                if ((int) expansion.size() != prev_size && prev_size >= 0) {
+                    cerr << endl
+                    << "*****" << endl
+                    << "*****ERROR: Each expanded column must have the same number of elements." << endl
+                    << "*****       This was violated at line: " << lineNum << endl
+                    << "*****" << endl;
+                    exit(1);
+                }
+                else {
+                    expandedCols.push_back(expansion);
+                }
+                prev_size = expansion.size();
+            }
+
+            // now replicate/expand the original line based on the 
+            // values in the requested columns
+            size_t totalCols  = inFields.size();
+            for (size_t n = 0; n < expandedCols[0].size(); n++) 
+            {
+                int numExpColsSeen = 0;
+                for (size_t c = 0; c < totalCols; c++)
+                {
+                    // normal column, print as-is
+                    if (!expColMap[c+1]) {
+                        printf("%s", inFields[c].c_str());
+                    }
+                    // expanded column, grab relevant value from expanded vector.
+                    else {
+                        printf("%s", expandedCols[numExpColsSeen][n].c_str());
+                        numExpColsSeen++;
+                    }
+                    // add a tab if not the very last value
+                    if (c < totalCols - 1)
+                        printf("\t");
+                }
+                printf("\n");
+            }
+        }
+        inFields.clear();
+    }
+    _tab->Close();
+}
+