CDS detector added

Former-commit-id: 93fac7a70052d06c2a12bf8af59820c653edd31b
Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076

detectors/cds/lib/translate.awk

@@ -0,0 +1,39 @@
+#
+# translate CDSs from iff file
+#
+
+BEGIN {
+  Seq = ReadFasta(FASTA)
+}
+
+/^c end_entry/ {
+  if (RevStrand) Cds = RevComplement(Cds)
+  Prot = Translate(substr(Cds, 1, length(Cds)-3))
+  if (Modif == "=")
+    Prot = "M" substr(Prot, 2)
+  print "e translate " Prot
+}
+
+{
+  print $0
+}
+
+/^c begin_entry/ {
+  Cds = ""
+  Iexon = 0
+  next
+}
+
+/^e exon/ {
+  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)
+    Cds = SubSeq(Seq, $3, $4) "" Cds
+  else
+    Cds = Cds "" SubSeq(Seq, $3, $4)
+  next
+}