Add a better management of and create translation exception when required for initiation codon

Former-commit-id: 878d919fdaad16e6e2645b62b3a53ef5d5e1ef2b
Former-commit-id: 3c3647cf114438a1ea9c3ff8c44e67e367929776

detectors/cds/lib/translate.awk

@@ -8,9 +8,16 @@ BEGIN {
 
 /^c end_entry/ {
   if (RevStrand) Cds = RevComplement(Cds)
-  Prot = Translate(substr(Cds, 1, length(Cds)-3))
-  if (Modif == "=")
-    Prot = "M" substr(Prot, 2)
+  Prot = Translate(substr(Cds, 1, length(Cds)-3),Modif,"chloroplast")
+
+  if (Modif == "=" && substr(Prot, 1,1) != "M") {
+    Prot = "M" substr(Prot, 2,length(Prot))
+    if (CdsStartPosFull==1) {
+      print "e trans_exception "CdsStartPos" Met"
+    } else {
+      print "e trans_exception " "ERROR" " Met"
+    }
+  }
   print "e translate " Prot
 }
 
@@ -21,19 +28,35 @@ BEGIN {
 /^c begin_entry/ {
   Cds = ""
   Iexon = 0
+  CdsStartPosFullv = 0
   next
 }
 
 /^e exon/ {
+  print "d cds " CDS
   RevStrand = ($6 == "-")
   if (++Iexon == 1) { # first is exon with start (even on - strand)
     Modif = $15
     gsub("\"", "", Modif)
     Modif = (RevStrand ? substr(Modif, 2, 1) : substr(Modif, 1, 1))
   }
-  if (RevStrand)
+  if (RevStrand){
     Cds = SubSeq(Seq, $3, $4) "" Cds
-  else
+    if (Iexon==1) {
+      if(($4 - $3 +1) >= 3) {
+        CdsStartPos="complement("$4-2".."$4")"
+        CdsStartPosFull=1
+      }
+    }}
+  else{
     Cds = Cds "" SubSeq(Seq, $3, $4)
+    if (Iexon==1) {
+      if (Iexon==1) {
+        if(($4 - $3 +1) >= 3) {
+          CdsStartPos=$3".."$3+2
+          CdsStartPosFull=1
+        }
+    }
+    }  }
   next
 }