new single strand option

@@ -17,7 +17,7 @@
 vector<int> multiFASTA_seqlen;
 vector<int> multiFASTA_seqlen;
 map<string, string> genetic_code;
 map<string, string> genetic_code;
 vector<string> sCodons;
 vector<string> sCodons;
-int minimum_length = 0;
+int minimum_length = 2; // dipeptides
 
 
 
 
 // XXX PROTOTYPES
 // XXX PROTOTYPES
@@ -200,6 +200,14 @@ int main(int argc, char** argv){
 	string optlist =
 	string optlist =
 		"    Usage:\n"
 		"    Usage:\n"
 		"\n"
 		"\n"
+		"    -i              Input file\n"
+		"    -o              Output filenames (default: input filename with .pro and .dna/.rna extensions)\n"
+		"    -s              Start codon\n"
+		"    -m              Minimum ORF length (default: 2)\n"
+		"    -a              Alternative genetic code\n"
+		"    -r              RNA input\n"
+		"    -c              Check FASTA format\n"
+		"    -f              Translate sense strand only\n" // f as in forward
 		"    -h              Help\n";
 		"    -h              Help\n";
 
 
 	string outFileName;
 	string outFileName;
@@ -208,10 +216,11 @@ int main(int argc, char** argv){
 	bool checkFASTA;
 	bool checkFASTA;
 	string alt_gene_code;
 	string alt_gene_code;
 	string startCodon;
 	string startCodon;
+	bool senseStrand;
 
 
 
 
 	int opt;
 	int opt;
-	while ((opt = getopt(argc,argv,"hrci:o:s:m:a:")) != EOF){
+	while ((opt = getopt(argc,argv,"hrcfi:o:s:m:a:")) != EOF){
 		switch(opt){
 		switch(opt){
 			case 'i': inFileName = optarg; break;
 			case 'i': inFileName = optarg; break;
 			case 'o': outFileName = optarg; break;
 			case 'o': outFileName = optarg; break;
@@ -220,6 +229,7 @@ int main(int argc, char** argv){
 			case 'a': alt_gene_code = optarg; break;
 			case 'a': alt_gene_code = optarg; break;
 			case 'r': rna = true; break;
 			case 'r': rna = true; break;
 			case 'c': checkFASTA = true; break;
 			case 'c': checkFASTA = true; break;
+			case 'f': senseStrand = true; break;
 			case 'h': fprintf(stderr, "%s", optlist.c_str()); return 0;
 			case 'h': fprintf(stderr, "%s", optlist.c_str()); return 0;
 		}
 		}
 	}
 	}
@@ -290,9 +300,20 @@ int main(int argc, char** argv){
 	puts("5'-3' translation...");
 	puts("5'-3' translation...");
 	(rna) ? genetic_code = gc_std : genetic_code = gc_std_DNA;
 	(rna) ? genetic_code = gc_std : genetic_code = gc_std_DNA;
 	translate_3_frames(inFileName, tmp_53_pro_file, tmp_53_dna_file, false);
 	translate_3_frames(inFileName, tmp_53_pro_file, tmp_53_dna_file, false);
+
+	// XXX DIRTY CLEANING
+	// awk '/^>/ {if (seq != "") {print head""seq;} seq=""; head=$0"\n";} /^[^>]/ {seq=seq""$0"\n";} END {if (seq != "") print head""seq;}' input.fasta > output.fasta
+	string command = "awk '/^>/ {if (seq != \"\") {print head\"\"seq;} seq=\"\"; head=$0\"\\n\";} /^[^>]/ {seq=seq\"\"$0\"\\n\";} END {if (seq != \"\") print head\"\"seq;}' "+ tmp_53_pro_file + " > " + output_pro + " && rm *.53pro *.53dna";
+	int status = std::system(command.c_str());
+	if (status != 0) {
+		std::cerr << "Error: system call failed with status " << status << std::endl;
+		return 1;
+	}
 	puts("Done");
 	puts("Done");
 
 
 
 
+	if (not senseStrand){
+		// TODO Warning for RNA sequence
 		/* Reversion of the input sequence by system call: rev + tac */
 		/* Reversion of the input sequence by system call: rev + tac */
 		puts("Genome reversion...");
 		puts("Genome reversion...");
 		if ( system( ("rev "+inFileName+" | tac > " + tmp_reversed_input).c_str() ) != 0 ){
 		if ( system( ("rev "+inFileName+" | tac > " + tmp_reversed_input).c_str() ) != 0 ){
@@ -335,8 +356,7 @@ int main(int argc, char** argv){
 		else{
 		else{
 			puts("Done");
 			puts("Done");
 		}
 		}
-
-
+	}