From 238b500e1aa04cf307db00fdc99db80429b1d5f9 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 24 Jan 2018 15:13:31 +0100
Subject: [PATCH] Add missing file...

Former-commit-id: f71b0396212bb8cd2df1ca1a4e5847f30c613a48
Former-commit-id: 17cc9616d8835548e996712545d4cc0e1833f90f
---
 detectors/cds/lib/cds.awk | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 detectors/cds/lib/cds.awk

diff --git a/detectors/cds/lib/cds.awk b/detectors/cds/lib/cds.awk
new file mode 100644
index 0000000..9ae4173
--- /dev/null
+++ b/detectors/cds/lib/cds.awk
@@ -0,0 +1,39 @@
+#
+# translate CDSs from iff file
+#
+
+BEGIN {
+  Seq = ReadFasta(FASTA)
+}
+
+/^c end_entry/ {
+  if (RevStrand) Cds = RevComplement(Cds)
+  DNA = substr(Cds, 1, length(Cds)-3)
+  print ">" genename 
+  for (i=1; i<=length(DNA); i+=60)
+  	print substr(DNA,i,60)
+}
+
+/^c annot/ {
+	genename=$3
+}
+
+/^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
+}