CDS detector added

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

detectors/cds/lib/libutil.awk

@@ -0,0 +1,179 @@
+#
+# utilities library
+#
+
+END {
+  if (_ForceExit_) exit(_ForceExit_)
+}
+
+function Notify(key, msg) {
+    print "# " key " " msg >> "/dev/stderr"
+}
+
+function Info(msg) {
+    Notify("info", msg)
+    return 1
+}
+
+function Warning(msg) {
+    Notify("warning", msg)
+    return 0
+}
+
+function Exit(status) {
+    exit(_ForceExit_ = status)
+}
+
+function Error(msg, status) {
+    Notify("error", msg)
+    Exit(status ? status : 1)
+}
+
+function Assert(condition, msg, status) {
+    if (! condition) {
+      msg = FILENAME ":" FNR ": " msg
+      return status ? Error(msg, status) : Warning(msg)
+    }
+}
+
+#
+
+function Min(a, b) {
+  return (a < b ? a : b)
+}
+
+function Max(a, b) {
+  return (a > b ? a : b)
+}
+
+#
+
+function Trim(s, regexp) {
+  if (regexp == 0) regexp = "[ \t]+"
+  gsub("^" regexp "|" regexp "$", "", s)
+  return s
+}
+
+function ShieldPath(path) {
+  gsub(" ", "\\ ", path)
+  return path
+}
+
+function TestPath(path, test, _local_, stat) {
+  if (test == 0) test = "-f"
+  if (Trim(path) == "")
+    return 0 # because of a bug in 'test'
+  stat = system("test " test " " ShieldPath(path))
+  return stat ? 0 : 1
+}
+
+#
+
+function Reverse(s, _local_, i, n, rs) {
+  rs = "";
+  n = length(s);
+  for (i = n ; i >= 1 ; i--)
+    rs = rs "" substr(s, i, 1)
+  return rs;
+}
+
+function RevComplement(seq, _local_, n, i, c, rs) {
+  n = length(seq)
+  rs = ""
+  for (i = n ; i >= 1 ; i--) {
+    c = substr(seq, i, 1)
+    rs = rs "" (_DnaC[c] ? _DnaC[c] : "X")
+  }
+  return rs
+}
+
+#
+
+function _AssertCode(name, _local_, n, i1, i2, i3, b1, b2, b3) {
+  if (_InitCod[name] != 0) return 1
+  for (i1 = 1 ; i1 <= 4 ; i1++) {
+    b1 = substr(_NucOrder, i1, 1)
+    for (i2 = 1 ; i2 <= 4 ; i2++) {
+      b2 = substr(_NucOrder, i2, 1)
+      for (i3 = 1 ; i3 <= 4 ; i3++) {
+        b3 = substr(_NucOrder, i3, 1)
+        _GenCod[name][b1 ""  b2 "" b3] = substr(_Cod2Aa[name], ++n, 1)
+      }
+    }
+  }
+  _InitCod[name] = 1
+  return 1
+}
+
+function Translate(seq, codname, _local_, n, i, c, p) {
+  if (codname == 0) codname = "universal"
+  _AssertCode(codname)
+  seq = toupper(seq)
+  n = length(seq)
+  p = ""
+  for (i = 1 ; i <= n ; i += 3) {
+    c = substr(seq, i, 3)
+    p = p "" ((c in _GenCod[codname]) ? _GenCod[codname][c] : "X")
+  }
+  return p
+}
+
+#
+
+function SubSeq(seq, from, to, revstrand) {
+  seq = substr(seq, from, to-from+1)
+  if (revstrand) seq = RevComplement(seq)
+  return seq
+}
+
+#
+
+function ReadFasta(file, _local_, seq, context) {
+  context = $0
+  seq = ""
+  getline < file
+  while(getline < file) seq = seq "" $0
+  $0 = context
+  return seq    
+}
+
+#
+
+function ReadModel(file, a, _local_, line, context) {
+  context = $0
+  delete a
+  while(getline < file)
+    if (! ($0 ~ "^#")) a[$1] = $2
+  $0 = context
+}
+
+#
+# constants
+#
+
+BEGIN {
+  # complementary of _IupacDna
+  _DnaC["A"] = "T"; _DnaC["C"] = "G"; _DnaC["G"] = "C"; _DnaC["T"] = "A"
+  _DnaC["R"] = "Y"; _DnaC["Y"] = "R"; _DnaC["M"] = "K"; _DnaC["K"] = "M"
+  _DnaC["W"] = "W"; _DnaC["S"] = "S"; _DnaC["B"] = "V"; _DnaC["V"] = "B"
+  _DnaC["D"] = "H"; _DnaC["H"] = "D"; _DnaC["N"] = "N"; _DnaC["X"] = "X"
+  _DnaC["a"] = "t"; _DnaC["c"] = "g"; _DnaC["g"] = "c"; _DnaC["t"] = "a"
+  _DnaC["r"] = "y"; _DnaC["y"] = "r"; _DnaC["m"] = "k"; _DnaC["k"] = "m"
+  _DnaC["w"] = "w"; _DnaC["s"] = "s"; _DnaC["b"] = "v"; _DnaC["v"] = "b"
+  _DnaC["d"] = "h"; _DnaC["h"] = "d"; _DnaC["n"] = "n"; _DnaC["x"] = "x"
+
+  # genetic codes
+  _NucOrder = "ACGT"
+                                #1  AAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTT
+                                #2  AAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTT
+                                #3  ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+  _Cod2Aa["universal"]           = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"
+  _Cod2Aa["mito-yeast"]          = "KNKNTTTTRSRSMIMIQHQHPPPPRRRRTTTTEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
+  _Cod2Aa["mito-vertebrates"]    = "KNKNTTTT*S*SMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
+  _Cod2Aa["mito-insects"]        = "KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
+  _Cod2Aa["mito-echinoderms"]    = "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"  
+  _Cod2Aa["mycoplasma"]          = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"
+  _Cod2Aa["ciliata"]             = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLF"
+  _Cod2Aa["euplotes"]            = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLF"
+  _Cod2Aa["candida"]             = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRXLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"
+}