0066211385
Former-commit-id: 412798e7efc6648f611fa205e893f097c1c3f583 Former-commit-id: daaa9808ca1990dda6cd137bb2ac3aaf1fb55600
143 lines
2.5 KiB
Awk
143 lines
2.5 KiB
Awk
#
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# iff -> embl
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#
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function FromLoc(i, _local_, s) {
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s = substr(Exon[i]["modif"], 1, 1) "" Exon[i]["from"]
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gsub("=", "", s)
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return s
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}
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function ToLoc(i, _local_, s) {
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s = substr(Exon[i]["modif"], 2, 1) "" Exon[i]["to"]
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gsub("=", "", s)
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return s
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}
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function GeneLocation(_local_, d, s) {
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d = Exon[1]["strand"]
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if (d == "+")
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s = FromLoc(1) ".." ToLoc(Nexon)
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else
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s = FromLoc(Nexon) ".." ToLoc(1)
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if (d == "-") s = "complement(" s ")"
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return s
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}
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function CdsLocation(_local_, d, i, s) {
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d = Exon[1]["strand"]
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if (d == "+") {
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for (i = 1 ; i <= Nexon ; i++)
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s = s "," FromLoc(i) ".." ToLoc(i)
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}
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else {
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for (i = Nexon ; i >= 1 ; i--)
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s = s "," FromLoc(i) ".." ToLoc(i)
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}
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s = substr(s, 2)
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if (Nexon > 1) s = "join(" s ")"
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if (d == "-") s = "complement(" s ")"
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return s
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}
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function ExonLocation(i, _local_, s) {
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s = FromLoc(i) ".." ToLoc(i)
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if (Exon[i]["strand"] == "-") s = "complement(" s ")"
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return s
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}
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function Pad(s, len) {
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while (length(s) < len)
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s = s " "
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return s
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}
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function Feature(feat, loc, _local_, s) {
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s = Pad("FT " feat, 21)
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print s "" loc
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}
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function SQualifier(qual, val, _local_, s) {
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s = Pad("FT", 21)
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print s "/" qual "=" val
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}
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function QQualifier(qual, val) {
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gsub("\"", "''", val)
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SQualifier(qual, "\"" val "\"")
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}
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#
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# rules
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#
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/^c annot/ {
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GeneName = $4
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Product = $NF
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gsub("_", " ", Product)
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next
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}
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/^c nclust/ {
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Ngene = $3
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next
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}
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/^c begin_entry/ {
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Nexon = 0
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delete Exon
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next
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}
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/^e exon/ {
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Nexon++
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Exon[Nexon]["from"] = $3
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Exon[Nexon]["to"] = $4
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Exon[Nexon]["strand"] = $6
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Exon[Nexon]["indels"] = $9 "+" $12
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modif = $15; gsub("\"", "", modif)
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Exon[Nexon]["modif"] = modif
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next
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}
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/^e similarity/ {
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split($12, a, "@")
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Simil = a[1] ":" a[2]
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next
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}
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/^e translate/ {
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Translat = $3
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next
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}
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/^c end_entry/ {
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gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
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locus = ""
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Feature("gene", GeneLocation())
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QQualifier("gene", gname)
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QQualifier("locus_tag", locus)
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Feature("CDS", CdsLocation())
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SQualifier("codon_start", 1)
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SQualifier("transl_table", 11)
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QQualifier("gene", gname)
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QQualifier("locus_tag", locus)
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QQualifier("product", Product)
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QQualifier("inference", "similar to DNA sequence:" Simil)
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QQualifier("translation", Translat)
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if (Nexon > 1) {
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for (i = 1 ; i <= Nexon ; i++) {
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Feature("exon", ExonLocation(i))
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QQualifier("gene", gname)
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QQualifier("locus_tag", locus)
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SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1)
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}
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}
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}
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