d77a0dfe67
Former-commit-id: 07fb256bf17db3f0ffc1730b0383f8255fbb9129 Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3
124 lines
2.7 KiB
Awk
124 lines
2.7 KiB
Awk
#
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# utilities library
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#
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function Min(a, b) {
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return (a < b ? a : b)
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}
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function Max(a, b) {
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return (a > b ? a : b)
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}
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function Strip(s) {
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gsub("complement|join|order|\\)|\\(|<|>| ", "", s)
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return s
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}
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function GetLoc(s, loc, _local_, a, tmp) {
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delete loc
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loc[1] = loc[2] = 0
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split(s, loc, "\\.\\.")
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if (loc[1] > loc[2]) {
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tmp = loc[1]
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loc[1] = loc[2]
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loc[2] = tmp
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}
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}
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function ParseLocation(s, locs, _local_, i, na, a, loc) {
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delete locs
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s = Strip(s)
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na = split(s, a, ",")
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for (i = 1 ; i <= na ; i++) {
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GetLoc(a[i], loc)
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locs[i][1] = loc[1]
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locs[i][2] = loc[2]
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}
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return na
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}
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function SpanLocation(s, sloc, _local_, i, na, locs) {
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delete sloc
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na = ParseLocation(s, locs)
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sloc[1] = (na > 0 ? locs[1][1] : 0)
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sloc[2] = (na > 0 ? locs[1][2] : 0)
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for (i = 2 ; i <= na ; i++) {
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sloc[1] = Min(sloc[1], locs[i][1])
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sloc[2] = Max(sloc[2], locs[i][2])
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}
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}
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function LenLocation(s, _local_, i, na, locs, len) {
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len = 0
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na = ParseLocation(s, locs)
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for (i = 1 ; i <= na ; i++) {
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len += locs[i][2] - locs[i][1] + 1
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}
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return len
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}
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function Nexons(s, _local_, a) {
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s = Strip(s)
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return split(s, a, ",")
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}
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function Reverse(s, _local_, i, n, rs) {
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rs = "";
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n = length(s);
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for (i = n ; i >= 1 ; i--)
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rs = rs "" substr(s, i, 1)
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return rs;
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}
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function RevComplement(seq, _local_, n, i, c, rs) {
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n = length(seq)
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rs = ""
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for (i = n ; i >= 1 ; i--) {
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c = substr(seq, i, 1)
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rs = rs "" (_DnaC[c] ? _DnaC[c] : "X")
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}
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return rs
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}
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function SubSeq(seq, from, to, revstrand) {
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seq = substr(seq, from, to-from+1)
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if (revstrand) seq = RevComplement(seq)
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return seq
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}
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function SeqLocation(seq, s, revstrand, _local_, sloc, i, na, locs) {
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sloc = ""
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na = ParseLocation(s, locs)
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for (i = 1 ; i <= na ; i++) {
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sloc = sloc "" SubSeq(seq, locs[i][1], locs[i][2], 0)
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}
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return (revstrand ? RevComplement(sloc) : sloc)
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}
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function GeneFamily(s) {
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s = tolower(s)
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gsub("(_|-)[0-9]+$", "", s)
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gsub("(_|-)(a|b|c|i)+$", "", s)
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gsub("'+$", "", s)
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gsub("/.+$", "", s)
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if (match(s, "[^a-z,0-9]")) s = "none"
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return s
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}
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#
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# constants
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#
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BEGIN {
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# complementary of _IupacDna
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_DnaC["A"] = "T"; _DnaC["C"] = "G"; _DnaC["G"] = "C"; _DnaC["T"] = "A"
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_DnaC["R"] = "Y"; _DnaC["Y"] = "R"; _DnaC["M"] = "K"; _DnaC["K"] = "M"
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_DnaC["W"] = "W"; _DnaC["S"] = "S"; _DnaC["B"] = "V"; _DnaC["V"] = "B"
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_DnaC["D"] = "H"; _DnaC["H"] = "D"; _DnaC["N"] = "N"; _DnaC["X"] = "X"
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_DnaC["a"] = "t"; _DnaC["c"] = "g"; _DnaC["g"] = "c"; _DnaC["t"] = "a"
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_DnaC["r"] = "y"; _DnaC["y"] = "r"; _DnaC["m"] = "k"; _DnaC["k"] = "m"
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_DnaC["w"] = "w"; _DnaC["s"] = "s"; _DnaC["b"] = "v"; _DnaC["v"] = "b"
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_DnaC["d"] = "h"; _DnaC["h"] = "d"; _DnaC["n"] = "n"; _DnaC["x"] = "x"
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}
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