98 lines
2.0 KiB
Awk
98 lines
2.0 KiB
Awk
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#
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# get cds features from embl (long version)
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#
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# -v FASTA
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# @include lib.embl.awk
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BEGIN {
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print "#locus locustag genefam gene from to strand nexon length status start stop dnaseq protseq product"
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if (HEADONLY != "") exit(0)
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if (MAXSPAN == "") MAXSPAN = 10000
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if (FASTA == "") Error("No FASTA file specified", 1)
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if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
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Seq = tolower(ReadFasta(FASTA))
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}
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/^ID / {
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locus = $2
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gsub(";", "", locus)
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incds = 0
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next
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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 locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
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nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, 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 locus, locustag, GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"),
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nexon, len, (ok ? "Ok" : "Error"), cstart, cstop, cdsseq, translation, product
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}
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}
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