fixed too many partial CDS bug

Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1
Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984

detectors/cds/tools/lib/compareCds.awk

@@ -0,0 +1,98 @@
+#
+#
+#
+
+function Min(a, b) {
+  return (a < b ? a : b)
+}
+
+function Max(a, b) {
+  return (a > b ? a : b)
+}
+
+function Align(s1, s2, _local_, d, l) {
+  if (s1 == s2) return 100
+  d = AlignNWS(s1, s2, Identity)
+  l = Max(length(s1), length(s2))
+  return int((l - d) * 100 / l)
+}
+
+BEGIN {
+  PROCINFO["sorted_in"] = "@ind_num_asc"
+  IdentityMatrix("ABCDEFGHIJKLMNOPQRSTUVWXYZ*", Identity)
+}
+
+BEGINFILE {
+  NFile++
+  File[NFile] = FILENAME
+}
+
+/^#/ { next }
+
+{
+  strand = $5
+  stop = (strand == "D" ? $4 : $3)
+  Stop[stop]++
+  i = ++NRec[NFile]
+  Rec[NFile][i]["record"] = $0
+  Rec[NFile][i]["genefam"] = $1
+  Rec[NFile][i]["gene"] = $2
+  Rec[NFile][i]["from"] = $3
+  Rec[NFile][i]["to"] = $4
+  Rec[NFile][i]["strand"] = $5
+  Rec[NFile][i]["nexon"] = $6
+  Rec[NFile][i]["length"] = $7
+  Rec[NFile][i]["protseq"] = $9
+  if (NFile == 1)
+    Indx1[stop] = i
+  else
+    Indx2[stop] = i
+}
+
+END {
+  for (st in Stop) {
+    if (Indx1[st])
+      print "FILE1 " Rec[1][Indx1[st]]["record"]
+    else 
+      print "FILE1 NONE"
+
+    if (Indx2[st])
+      print "FILE2 " Rec[2][Indx2[st]]["record"]
+    else 
+      print "FILE2 NONE"
+      
+    if (Indx1[st] && Indx2[st]) {
+      fm = Rec[1][Indx1[st]]["genefam"]
+      id = Align(Rec[1][Indx1[st]]["protseq"], Rec[2][Indx2[st]]["protseq"])
+      printf("MATCH %s ID %d ", fm, id)
+      if (id == 100)
+        status = "CORRECT"
+      else if (id >= 90)
+        status = "ALMOST_CORRECT"
+      else if (id >= 80)
+        status = "ACCEPTABLE"
+      else
+        status = "WRONG"
+      if (status != "CORRECT") {
+        if (Rec[1][Indx1[st]]["nexon"] != Rec[2][Indx2[st]]["nexon"])
+          status = status ".BAD_NBEXON"
+        start1 = Rec[1][Indx1[st]]["strand"] == "D" ? Rec[1][Indx1[st]]["from"] : Rec[1][Indx1[st]]["to"]
+        start2 = Rec[2][Indx2[st]]["strand"] == "D" ? Rec[2][Indx2[st]]["from"] : Rec[2][Indx2[st]]["to"]
+        if (start1 != start2)
+          status = status ".BAD_START"
+        else
+          status = status ".BAD_JUNCTION"
+      }
+      print status
+    }
+    else if (Indx1[st]) {
+      fm = Rec[1][Indx1[st]]["genefam"]
+      print "MATCH " fm " ID 0 MISSED.WRONG_STOP"
+    }
+    else if (Indx2[st]) {
+      fm = Rec[2][Indx2[st]]["genefam"]
+      print "MATCH " fm " ID 0 OVERPRED.WRONG_STOP"
+    }
+    print ""
+  }
+}