d77a0dfe67
Former-commit-id: 07fb256bf17db3f0ffc1730b0383f8255fbb9129 Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3
81 lines
1.6 KiB
Awk
81 lines
1.6 KiB
Awk
#
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# get cds features from embl (short version)
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#
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# @include lib.embl.awk
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BEGIN {
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if (MAXSPAN == "") MAXSPAN = 10000
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print "#genefam gene from to strand nexon length status protseq product"
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}
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/^FT CDS/ {
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revstrand = match($3, "^complement")
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s = substr($0, 22)
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gsub("^complement", "", s)
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ok = ! match(s, "complement|order")
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nexon = Nexons(s)
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SpanLocation(s, sloc)
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spanlen = sloc[2] - sloc[1] + 1
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len = LenLocation(s)
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ok = ok && (len < MAXSPAN)
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cdsseq = ok ? SeqLocation(seq, s, revstrand) : "XXX"
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cstart = substr(cdsseq, 1,3)
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cstop = substr(cdsseq, length(cdsseq)-2)
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gene = "none"
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locustag = "none"
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product = "none"
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translation = "X"
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incds = 1
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next
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}
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(incds && /^FT [^ ]/) {
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print GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
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nexon, len, (ok ? "Ok" : "Error"), translation, product
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incds = 0
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next
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}
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/^FT \/gene=/ {
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split($0, a, "=")
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gene = a[2]
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gsub("^[^a-z,A-Z]+", "", gene)
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gsub("\"", "", gene)
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gsub(" ", "_", gene)
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next
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}
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/^FT \/locus_tag=/ {
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split($0, a, "=")
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locustag = a[2]
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gsub("\"", "", locustag)
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gsub(" ", "_", locustag)
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next
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}
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/^FT \/product=/ {
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split($0, a, "=")
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product = a[2]
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gsub("\"", "", product)
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gsub(" ", "_", product)
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next
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}
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/^FT \/translation=/ {
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split($0, a, "=")
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translation = a[2]
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gsub("\"", "", translation)
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gsub(" ", "", translation)
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next
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}
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END {
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if (incds) {
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print GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
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nexon, len, (ok ? "Ok" : "Error"), translation, product
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}
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}
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