alter gen codes

@@ -3,10 +3,10 @@ BruteSmORF
 
 
 
-Exhaustive approach for solving difficult cases of small open reading frame annotation: the PreImplantation Factor case
+Exhaustive approach for solving difficult cases of small open reading frame annotation: the PreImplantation Factor example
 
 
-The PreImplantation Factor: a difficult cases of small open reading frame annotation solved by an exhaustive approach
+The PreImplantation Factor: a difficult case of small open reading frame annotation solved by an exhaustive approach
 
 
 

+
+
+mutli-FASTA
+
+display name of alternate genetic code
+
+
+
+

+void select_genetic_code(string selection){
+	cout << "Genetic code selected: " << selection << endl;
+	// The Vertebrate Mitochondrial Code
+	if (selection == "2"){
+		gc_std["AGA"] = "*"; gc_std_DNA["AGA"] = "*"; gc_std_rev["UCU"] = "*"; gc_std_DNA_rev["TCT"] = "*";
+		gc_std["AGG"] = "*"; gc_std_DNA["AGG"] = "*"; gc_std_rev["UCC"] = "*"; gc_std_DNA_rev["TCC"] = "*";
+		gc_std["AGR"] = "*"; gc_std_DNA["AGR"] = "*"; gc_std_rev["UCY"] = "*"; gc_std_DNA_rev["TCY"] = "*";
+		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "3"){
+		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
+		gc_std["CUU"] = "T"; gc_std_DNA["CTT"] = "T"; gc_std_rev["GAA"] = "T"; gc_std_DNA_rev["GAA"] = "T";
+		gc_std["CUC"] = "T"; gc_std_DNA["CTC"] = "T"; gc_std_rev["GAG"] = "T"; gc_std_DNA_rev["GAG"] = "T";
+		gc_std["CUA"] = "T"; gc_std_DNA["CTA"] = "T"; gc_std_rev["GAU"] = "T"; gc_std_DNA_rev["GAT"] = "T";
+		gc_std["CUG"] = "T"; gc_std_DNA["CTG"] = "T"; gc_std_rev["GAC"] = "T"; gc_std_DNA_rev["GAC"] = "T";
+		gc_std["CUN"] = "T"; gc_std_DNA["CTN"] = "T"; gc_std_rev["GAN"] = "T"; gc_std_DNA_rev["GAN"] = "T";
+		gc_std["CUR"] = "T"; gc_std_DNA["CTR"] = "T"; gc_std_rev["GAR"] = "T"; gc_std_DNA_rev["GAR"] = "T";
+		gc_std["CUY"] = "T"; gc_std_DNA["CTY"] = "T"; gc_std_rev["GAY"] = "T"; gc_std_DNA_rev["GAY"] = "T";
+		gc_std["CUM"] = "T"; gc_std_DNA["CTM"] = "T"; gc_std_rev["GAM"] = "T"; gc_std_DNA_rev["GAM"] = "T";
+		gc_std["CUK"] = "T"; gc_std_DNA["CTK"] = "T"; gc_std_rev["GAK"] = "T"; gc_std_DNA_rev["GAK"] = "T";
+		gc_std["CUS"] = "T"; gc_std_DNA["CTS"] = "T"; gc_std_rev["GAS"] = "T"; gc_std_DNA_rev["GAS"] = "T";
+		gc_std["CUW"] = "T"; gc_std_DNA["CTW"] = "T"; gc_std_rev["GAW"] = "T"; gc_std_DNA_rev["GAW"] = "T";
+		gc_std["CUH"] = "T"; gc_std_DNA["CTH"] = "T"; gc_std_rev["GAH"] = "T"; gc_std_DNA_rev["GAH"] = "T";
+		gc_std["CUB"] = "T"; gc_std_DNA["CTB"] = "T"; gc_std_rev["GAB"] = "T"; gc_std_DNA_rev["GAB"] = "T";
+		gc_std["CUV"] = "T"; gc_std_DNA["CTV"] = "T"; gc_std_rev["GAV"] = "T"; gc_std_DNA_rev["GAV"] = "T";
+		gc_std["CUD"] = "T"; gc_std_DNA["CTD"] = "T"; gc_std_rev["GAD"] = "T"; gc_std_DNA_rev["GAD"] = "T";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "4"){ // Mycoplasma
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "5"){
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
+		gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
+		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "6"){
+		gc_std["UAA"] = "Q"; gc_std_DNA["TAA"] = "Q"; gc_std_rev["AUU"] = "Q"; gc_std_DNA_rev["ATT"] = "Q";
+		gc_std["UAG"] = "Q"; gc_std_DNA["TAG"] = "Q"; gc_std_rev["AUC"] = "Q"; gc_std_DNA_rev["ATC"] = "Q";
+		gc_std["UAR"] = "Q"; gc_std_DNA["TAR"] = "Q"; gc_std_rev["AUY"] = "Q"; gc_std_DNA_rev["ATY"] = "Q";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "9"){
+		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
+		gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "10"){
+		gc_std["UGA"] = "C"; gc_std_DNA["TGA"] = "C"; gc_std_rev["ACU"] = "C"; gc_std_DNA_rev["ACT"] = "C";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "12"){
+		gc_std["CUG"] = "S"; gc_std_DNA["CTG"] = "S"; gc_std_rev["GAC"] = "S"; gc_std_DNA_rev["GAC"] = "S";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "13"){
+		gc_std["AGA"] = "G"; gc_std_DNA["AGA"] = "G"; gc_std_rev["UCU"] = "G"; gc_std_DNA_rev["TCT"] = "G";
+		gc_std["AGG"] = "G"; gc_std_DNA["AGG"] = "G"; gc_std_rev["UCC"] = "G"; gc_std_DNA_rev["TCC"] = "G";
+		gc_std["AGR"] = "G"; gc_std_DNA["AGR"] = "G"; gc_std_rev["UCY"] = "G"; gc_std_DNA_rev["TCY"] = "G";
+		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "14"){
+		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
+		gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
+		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "16"){
+		gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "21"){
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
+		gc_std["AGR"] = "S"; gc_std_DNA["AGR"] = "S"; gc_std_rev["UCY"] = "S"; gc_std_DNA_rev["TCY"] = "S";
+		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "22"){
+		gc_std["UCA"] = "*"; gc_std_DNA["TCA"] = "*"; gc_std_rev["AGU"] = "*"; gc_std_DNA_rev["AGT"] = "*";
+		gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "23"){
+		gc_std["UUA"] = "*"; gc_std_DNA["TTA"] = "*"; gc_std_rev["AAU"] = "*"; gc_std_DNA_rev["AAT"] = "*";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "24"){
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "25"){
+		gc_std["UGA"] = "G"; gc_std_DNA["TGA"] = "G"; gc_std_rev["ACU"] = "G"; gc_std_DNA_rev["ACT"] = "G";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "26"){
+		gc_std["CUG"] = "A"; gc_std_DNA["CTG"] = "A"; gc_std_rev["GAC"] = "A"; gc_std_DNA_rev["GAC"] = "A";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "29"){
+		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
+		gc_std["UAG"] = "Y"; gc_std_DNA["TAG"] = "Y"; gc_std_rev["AUC"] = "Y"; gc_std_DNA_rev["ATC"] = "Y";
+		gc_std["UAR"] = "Y"; gc_std_DNA["TAR"] = "Y"; gc_std_rev["AUY"] = "Y"; gc_std_DNA_rev["ATY"] = "Y";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "30"){
+		gc_std["UAA"] = "E"; gc_std_DNA["TAA"] = "E"; gc_std_rev["AUU"] = "E"; gc_std_DNA_rev["ATT"] = "E";
+		gc_std["UAG"] = "E"; gc_std_DNA["TAG"] = "E"; gc_std_rev["AUC"] = "E"; gc_std_DNA_rev["ATC"] = "E";
+		gc_std["UAR"] = "E"; gc_std_DNA["TAR"] = "E"; gc_std_rev["AUY"] = "E"; gc_std_DNA_rev["ATY"] = "E";
+	}
+	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+	else if (selection == "33"){
+		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
+		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
+		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
+		gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
+	}
+}
+
+// -11,  (-27, -28, -31)
+
+
+                                        // N R Y M K S W H B V D
+                                        // N Y R K M S W D V B H
+
+

@@ -7,6 +7,7 @@
 #include <algorithm>
 #include <vector>
 #include "split.h"
+#include "alternate_codes.h"
 
 // system detection
 // docker
@@ -15,12 +16,35 @@
 /* Global variables */
 vector<int> multiFASTA_seqlen;
 map<string, string> genetic_code;
-vector<string> sCodon;
+vector<string> sCodons;
 int minimum_length = 0;
 
 
 // XXX PROTOTYPES
 
+vector<string> complement_sCodons(vector<string> vec_codons, bool rna){
+	vector<string> cvec_codons;
+	for (string sCodon : vec_codons){
+		string codonCompl;
+		for (char& c : sCodon){
+			if (c == 'A'){
+				(rna) ? codonCompl+='U' : codonCompl+='T';
+			}
+			if (c == 'C'){
+				codonCompl+='G';
+			}
+			if (c == 'G'){
+				codonCompl+='C';
+			}
+			if (c == 'T'){
+				codonCompl+='A';
+			}
+		}
+		cvec_codons.push_back(codonCompl);
+	}
+	return cvec_codons;
+}
+
 
 void extend_until_print(string &codon, string &protein, string &nucleic, int frame, char posneg, ofstream &outfile, ofstream &outfileDNA, bool backward, int position, int glob_vec_index){
 	if (codon.length() == 3){
@@ -42,8 +66,8 @@ void extend_until_print(string &codon, string &protein, string &nucleic, int fra
 
 					//reverse( nucleic.begin(), nucleic.end() ); // XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX XXX
 
-					if (!sCodon.empty()){
-						if (find(sCodon.begin(), sCodon.end(), nucleic.substr(0, 3)) != sCodon.end()){ // if nucleic codon is in the vector of start codons
+					if (!sCodons.empty()){
+						if (find(sCodons.begin(), sCodons.end(), nucleic.substr(0, 3)) != sCodons.end()){ // if nucleic codon is in the vector of start codons
 							outfile << frame << posneg << "\t" << begin << "-" << position << "\t" << protein << "\n";
 							outfileDNA << frame << posneg << "\t" << begin << "-" << position << "\t" << nucleic << "\n";
 						}
@@ -169,126 +193,6 @@ int check_file_content(string fastaFileName, bool rna){
 }
 
 
-void select_genetic_code(string selection){
-	cout << "Genetic code selected: " << selection << endl;
-	// The Vertebrate Mitochondrial Code
-	if (selection == "2"){
-		gc_std["AGA"] = "*"; gc_std_DNA["AGA"] = "*"; gc_std_rev["UCU"] = "*"; gc_std_DNA_rev["TCT"] = "*";
-		gc_std["AGG"] = "*"; gc_std_DNA["AGG"] = "*"; gc_std_rev["UCC"] = "*"; gc_std_DNA_rev["TCC"] = "*";
-		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "3"){
-		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
-		gc_std["CUU"] = "T"; gc_std_DNA["CTT"] = "T"; gc_std_rev["GAA"] = "T"; gc_std_DNA_rev["GAA"] = "T";
-		gc_std["CUC"] = "T"; gc_std_DNA["CTC"] = "T"; gc_std_rev["GAG"] = "T"; gc_std_DNA_rev["GAG"] = "T";
-		gc_std["CUA"] = "T"; gc_std_DNA["CTA"] = "T"; gc_std_rev["GAU"] = "T"; gc_std_DNA_rev["GAT"] = "T";
-		gc_std["CUG"] = "T"; gc_std_DNA["CTG"] = "T"; gc_std_rev["GAC"] = "T"; gc_std_DNA_rev["GAC"] = "T";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "4"){ // Mycoplasma
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "5"){
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
-		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "6"){
-		gc_std["UAA"] = "Q"; gc_std_DNA["TAA"] = "Q"; gc_std_rev["AUU"] = "Q"; gc_std_DNA_rev["ATT"] = "Q";
-		gc_std["UAG"] = "Q"; gc_std_DNA["TAG"] = "Q"; gc_std_rev["AUC"] = "Q"; gc_std_DNA_rev["ATC"] = "Q";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "9"){
-		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "10"){
-		gc_std["UGA"] = "C"; gc_std_DNA["TGA"] = "C"; gc_std_rev["ACU"] = "C"; gc_std_DNA_rev["ACT"] = "C";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "12"){
-		gc_std["CUG"] = "S"; gc_std_DNA["CTG"] = "S"; gc_std_rev["GAC"] = "S"; gc_std_DNA_rev["GAC"] = "S";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "13"){
-		gc_std["AGA"] = "G"; gc_std_DNA["AGA"] = "G"; gc_std_rev["UCU"] = "G"; gc_std_DNA_rev["TCT"] = "G";
-		gc_std["AGG"] = "G"; gc_std_DNA["AGG"] = "G"; gc_std_rev["UCC"] = "G"; gc_std_DNA_rev["TCC"] = "G";
-		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "14"){
-		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
-		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "16"){
-		gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "21"){
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-		gc_std["AUA"] = "M"; gc_std_DNA["ATA"] = "M"; gc_std_rev["UAU"] = "M"; gc_std_DNA_rev["TAT"] = "M";
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "S"; gc_std_DNA["AGG"] = "S"; gc_std_rev["UCC"] = "S"; gc_std_DNA_rev["TCC"] = "S";
-		gc_std["AAA"] = "N"; gc_std_DNA["AAA"] = "N"; gc_std_rev["UUU"] = "N"; gc_std_DNA_rev["TTT"] = "N";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "22"){
-		gc_std["UCA"] = "*"; gc_std_DNA["TCA"] = "*"; gc_std_rev["AGU"] = "*"; gc_std_DNA_rev["AGT"] = "*";
-		gc_std["UAG"] = "L"; gc_std_DNA["TAG"] = "L"; gc_std_rev["AUC"] = "L"; gc_std_DNA_rev["ATC"] = "L";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "23"){
-		gc_std["UUA"] = "*"; gc_std_DNA["TTA"] = "*"; gc_std_rev["AAU"] = "*"; gc_std_DNA_rev["AAT"] = "*";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "24"){
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "25"){
-		gc_std["UGA"] = "G"; gc_std_DNA["TGA"] = "G"; gc_std_rev["ACU"] = "G"; gc_std_DNA_rev["ACT"] = "G";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "26"){
-		gc_std["CUG"] = "A"; gc_std_DNA["CTG"] = "A"; gc_std_rev["GAC"] = "A"; gc_std_DNA_rev["GAC"] = "A";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "29"){
-		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
-		gc_std["UAG"] = "Y"; gc_std_DNA["TAG"] = "Y"; gc_std_rev["AUC"] = "Y"; gc_std_DNA_rev["ATC"] = "Y";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "30"){
-		gc_std["UAA"] = "E"; gc_std_DNA["TAA"] = "E"; gc_std_rev["AUU"] = "E"; gc_std_DNA_rev["ATT"] = "E";
-		gc_std["UAG"] = "E"; gc_std_DNA["TAG"] = "E"; gc_std_rev["AUC"] = "E"; gc_std_DNA_rev["ATC"] = "E";
-	}
-	// xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-	else if (selection == "33"){
-		gc_std["UAA"] = "Y"; gc_std_DNA["TAA"] = "Y"; gc_std_rev["AUU"] = "Y"; gc_std_DNA_rev["ATT"] = "Y";
-		gc_std["UGA"] = "W"; gc_std_DNA["TGA"] = "W"; gc_std_rev["ACU"] = "W"; gc_std_DNA_rev["ACT"] = "W";
-		gc_std["AGA"] = "S"; gc_std_DNA["AGA"] = "S"; gc_std_rev["UCU"] = "S"; gc_std_DNA_rev["TCT"] = "S";
-		gc_std["AGG"] = "K"; gc_std_DNA["AGG"] = "K"; gc_std_rev["UCC"] = "K"; gc_std_DNA_rev["TCC"] = "K";
-	}
-}
-
-// -11,  (-27, -28, -31)
-
 // input list of files XXX
 
 
@@ -344,7 +248,8 @@ int main(int argc, char** argv){
 		puts("Start codon: no specific amino acid selected");
 	}
 	else{
-		sCodon = split(startCodon, '-');
+		sCodons = split(startCodon, '-');
+		// XXX Check alternate
 	}
 
 	/* Check input file content */
@@ -361,8 +266,7 @@ int main(int argc, char** argv){
 
 	/* Modifications to the standard genetic code */
 	select_genetic_code(alt_gene_code);
-	// XXX option pour Alternative Initiation Codons
-	// OU BIEN fichier txt lu
+	// XXX Check value
 
 
 	/* Filenames: temporary AND final output */
@@ -406,6 +310,7 @@ int main(int argc, char** argv){
 	/* Translation 3'-5' */
 	puts("3'-5' translation...");
 	(rna) ? genetic_code = gc_std_rev : genetic_code = gc_std_DNA_rev;
+	sCodons = complement_sCodons(sCodons, rna);
 	translate_3_frames(tmp_reversed_input, tmp_35_pro_file, tmp_35_dna_file, true);
 	puts("Done");