98 lines
1.3 KiB
Awk
98 lines
1.3 KiB
Awk
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#
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# get feature info from genbank
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#
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# @include libgbk.awk
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function GC(s, _local_, i, len) {
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s = toupper(s)
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len = length(s)
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gsub("G|C", "", s)
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return ((len - length(s)) * 100 / len)
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}
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#
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# rules
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#
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BEGIN {
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print "#locus orga len oklen gc nbCds nbCds_int0 nbCds_int1 nbCds_intsup1 perCds_noex meanCdsSize nbtRNA nbrRNA nboRNA"
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}
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/^LOCUS/ {
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locus = $2
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next
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}
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/^ ORGANISM/ {
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orga = substr($0, 13)
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split(orga, a, ";")
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orga = a[1]
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gsub(" ", "_", orga)
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next
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}
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/^ source/ {
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GetLoc($2, loc);
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len = loc[2];
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next
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}
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/^ CDS/ {
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meanCds = meanCds * nbCds + LenLocation($2)
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nbCds++
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meanCds /= nbCds
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n = Nexons($2)
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if (n > 3) n = 3
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nbCdx[n]++
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next
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}
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/^ tRNA/ {
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nbTrna++
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next
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}
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/^ rRNA/ {
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nbRrna++
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next
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}
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/^ mRNA/ {
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next
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}
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/^ .*RNA/ {
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nbOrna++
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next
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}
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/^ORIGIN/ {
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inseq = 1
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seq = ""
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next
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}
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inseq && /^ +[1-9][0-9]*/ {
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s = substr($0, 11)
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gsub(" ", "", s)
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seq = seq "" s
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next
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}
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/^\/\// {
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oklen = (len == length(seq) ? "ok" : "wrong")
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gc = GC(seq)
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print locus, orga, len, oklen, gc, nbCds+0, nbCdx[1]+0, \
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nbCdx[2]+0, nbCdx[3]+0, (nbCdx[1]+0)*100/Max(1, nbCds+0), \
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meanCds+0, nbTrna+0, nbRrna+0, nbOrna+0
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nbCds = nbTrna = nbRrna = nbOrna = len = inseq = meanCds = 0
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delete nbCdx
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orga = locus = "?"
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}
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