Added -full to fastaFromBed

src/fastaFromBed/fastaFromBed.cpp

@@ -13,38 +13,17 @@
 #include "fastaFromBed.h"
 
 
-Bed2Fa::Bed2Fa(bool &useName, string &dbFile, string &bedFile,
-    string &fastaOutFile, bool &useFasta, bool &useStrand) {
-
-    if (useName) {
-        _useName = true;
-    }
+Bed2Fa::Bed2Fa(const string &dbFile, const string &bedFile, bool useFasta, bool useStrand, bool useName, bool useFull) {
 
     _dbFile       = dbFile;
     _bedFile      = bedFile;
-    _fastaOutFile = fastaOutFile;
     _useFasta     = useFasta;
     _useStrand    = useStrand;
+    _useName      = useName;
+    _useFull      = useFull;
 
     _bed = new BedFile(_bedFile);
 
-    // Figure out what the output file should be.
-    if (fastaOutFile == "stdout") {
-        _faOut = &cout;
-    }
-    else {
-        // Make sure we can open the file.
-        ofstream fa(fastaOutFile.c_str(), ios::out);
-        if ( !fa ) {
-            cerr << "Error: The requested fasta output file (" << fastaOutFile << ") could not be opened. Exiting!" << endl;
-            exit (1);
-        }
-        else {
-            fa.close();
-            _faOut = new ofstream(fastaOutFile.c_str(), ios::out);
-        }
-    }
-
     // Extract the requested intervals from the FASTA input file.
     ExtractDNA();
 }
@@ -66,22 +45,28 @@ void Bed2Fa::ReportDNA(const BED &bed, string &dna) {
     if (!(_useName)) {
         if (_useFasta == true) {
             if (_useStrand == true)
-                *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end   << "(" << bed.strand << ")" << endl << dna << endl;
+                cout << ">" << bed.chrom << ":" << bed.start << "-" << bed.end   << "(" << bed.strand << ")" << endl << dna << endl;
             else
-                *_faOut << ">" << bed.chrom << ":" << bed.start << "-" << bed.end << endl << dna << endl;
+                cout << ">" << bed.chrom << ":" << bed.start << "-" << bed.end << endl << dna << endl;
         }
         else {
-            if (_useStrand == true)
-                *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "(" << bed.strand << ")" << "\t" << dna << endl;
-            else
-                *_faOut << bed.chrom << ":" << bed.start << "-" << bed.end << "\t" << dna << endl;
+            if (_useFull == true) {
+                _bed->reportBedTab(bed);
+                cout << dna << endl;
+            }
+            else {
+                if (_useStrand == true)
+                    cout << bed.chrom << ":" << bed.start << "-" << bed.end << "(" << bed.strand << ")" << "\t" << dna << endl;
+                else
+                    cout << bed.chrom << ":" << bed.start << "-" << bed.end << "\t" << dna << endl;
+            }
         }
     }
     else {
         if (_useFasta == true)
-            *_faOut << ">" << bed.name << endl << dna << endl;
+            cout << ">" << bed.name << endl << dna << endl;
         else
-            *_faOut << bed.name << "\t" << dna << endl;
+            cout << bed.name << "\t" << dna << endl;
     }
 }
 

src/fastaFromBed/fastaFromBed.h

@@ -29,8 +29,8 @@ class Bed2Fa {
 public:
 
     // constructor
-    Bed2Fa(bool &useName, string &dbFile, string &bedFile, string &fastaOutFile,
-        bool &useFasta, bool &useStrand);
+    Bed2Fa(const string &dbFile, const string &bedFile, 
+           bool useFasta, bool useStrand, bool useName, bool useFull);
 
     // destructor
     ~Bed2Fa(void);
@@ -40,17 +40,15 @@ public:
 
 
 private:
-
-    bool _useName;
     string _dbFile;
     string _bedFile;
-    string _fastaOutFile;
     bool _useFasta;
-    bool _useStrand;
+    bool _useStrand;  // should we extract a specific strand?
+    bool _useName;    // should we use the BED name for the FASTA header?
+    bool _useFull;    // should we use the full BED entry for the tabular output?
 
     // instance of a bed file class.
     BedFile  *_bed;
-    ostream *_faOut;
 };
 
 #endif

src/fastaFromBed/fastaFromBedMain.cpp

@@ -39,8 +39,8 @@ int main(int argc, char* argv[]) {
     // checks for existence of parameters
     bool haveFastaDb = false;
     bool haveBed = false;
-    bool haveFastaOut = false;
     bool useNameOnly = false;
+    bool useFullBedEntry = false;
     bool useFasta = true;
     bool useStrand = false;
 
@@ -70,13 +70,6 @@ int main(int argc, char* argv[]) {
                 i++;
             }
         }
-        else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFastaOut = true;
-                fastaOutFile = argv[i + 1];
-                i++;
-            }
-        }
         else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
             if ((i+1) < argc) {
                 haveBed = true;
@@ -87,6 +80,10 @@ int main(int argc, char* argv[]) {
         else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
             useNameOnly = true;
         }
+        else if(PARAMETER_CHECK("-full", 5, parameterLength)) {
+            useFullBedEntry = true;
+            useFasta = false;
+        }
         else if(PARAMETER_CHECK("-tab", 4, parameterLength)) {
             useFasta = false;
         }
@@ -99,13 +96,17 @@ int main(int argc, char* argv[]) {
         }
     }
 
-    if (!haveFastaDb || !haveFastaOut || !haveBed) {
+    if (!haveFastaDb || !haveBed) {
+        showHelp = true;
+    }
+    if (useFullBedEntry && useNameOnly) {
+        cerr << "*****ERROR: Cannot use both -name and -full. Choose one or the other.*****" << endl << endl;
         showHelp = true;
     }
 
     if (!showHelp) {
 
-        Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile, useFasta, useStrand);
+        Bed2Fa *b2f = new Bed2Fa(fastaDbFile, bedFile, useFasta, useStrand, useNameOnly, useFullBedEntry);
         delete b2f;
 
         return 0;
@@ -123,16 +124,16 @@ void ShowHelp(void) {
 
     cerr << "Summary: Extract DNA sequences into a fasta file based on feature coordinates." << endl << endl;
 
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf> -fo <fasta> " << 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;
     cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl;
-    cerr << "\t-fo\tOutput file (can be FASTA or TAB-delimited)" << endl;
     cerr << "\t-name\tUse the name field for the FASTA header" << endl;
 
     cerr << "\t-tab\tWrite output in TAB delimited format." << endl;
     cerr << "\t\t- Default is FASTA format." << endl << endl;
+    cerr << "\t-full\tUse the full BED entry when using -tab. Default is chr:start-end." << endl;
 
     cerr << "\t-s\tForce strandedness. If the feature occupies the antisense strand," << endl;
     cerr << "\t\tthe sequence will be reverse complemented." << endl;