added cds/tools/compare

Former-commit-id: 07fb256bf17db3f0ffc1730b0383f8255fbb9129
Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3

detectors/cds/tools/compare/lib/libutil.awk

@@ -0,0 +1,123 @@
+#
+# utilities library
+#
+
+function Min(a, b) {
+  return (a < b ? a : b)
+}
+
+function Max(a, b) {
+  return (a > b ? a : b)
+}
+
+function Strip(s) {
+  gsub("complement|join|order|\\)|\\(|<|>| ", "", s)
+  return s
+}
+
+function GetLoc(s, loc, _local_, a, tmp) {
+  delete loc
+  loc[1] = loc[2] = 0
+  split(s, loc, "\\.\\.")
+  if (loc[1] > loc[2]) {
+    tmp = loc[1]
+    loc[1] = loc[2]
+    loc[2] = tmp
+  }
+}
+
+function ParseLocation(s, locs, _local_, i, na, a, loc) {
+  delete locs
+  s = Strip(s)
+  na = split(s, a, ",")
+  for (i = 1 ; i <= na ; i++) {
+    GetLoc(a[i], loc)
+    locs[i][1] = loc[1]
+    locs[i][2] = loc[2]
+  }
+  return na
+}
+
+function SpanLocation(s, sloc, _local_, i, na, locs) {
+  delete sloc
+  na = ParseLocation(s, locs)
+  sloc[1] = (na > 0 ? locs[1][1] : 0)
+  sloc[2] = (na > 0 ? locs[1][2] : 0)
+  for (i = 2 ; i <= na ; i++) {
+    sloc[1] = Min(sloc[1], locs[i][1])
+    sloc[2] = Max(sloc[2], locs[i][2])
+  }
+}
+
+function LenLocation(s, _local_, i, na, locs, len) {
+  len = 0
+  na = ParseLocation(s, locs)
+  for (i = 1 ; i <= na ; i++) {
+    len += locs[i][2] - locs[i][1] + 1
+  }
+  return len
+}
+
+function Nexons(s, _local_, a) {
+  s = Strip(s)
+  return split(s, a, ",")
+}
+
+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 SubSeq(seq, from, to, revstrand) {
+  seq = substr(seq, from, to-from+1)
+  if (revstrand) seq = RevComplement(seq)
+  return seq
+}
+
+function SeqLocation(seq, s, revstrand, _local_, sloc, i, na, locs) {
+  sloc = ""
+  na = ParseLocation(s, locs)
+  for (i = 1 ; i <= na ; i++) {
+    sloc = sloc "" SubSeq(seq, locs[i][1], locs[i][2], 0)
+  }
+  return (revstrand ? RevComplement(sloc) : sloc)
+}
+
+function GeneFamily(s) {
+  s = tolower(s)
+  gsub("(_|-)[0-9]+$", "", s)
+  gsub("(_|-)(a|b|c|i)+$", "", s)
+  gsub("'+$", "", s)
+  gsub("/.+$", "", s)
+  if (match(s, "[^a-z,0-9]")) s = "none"
+  return s
+}
+
+#
+# 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"
+}