40 lines
663 B
Awk
40 lines
663 B
Awk
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#
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# translate CDSs from iff file
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#
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BEGIN {
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Seq = ReadFasta(FASTA)
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}
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/^c end_entry/ {
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if (RevStrand) Cds = RevComplement(Cds)
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DNA = substr(Cds, 1, length(Cds)-3)
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print ">" genename
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for (i=1; i<=length(DNA); i+=60)
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print substr(DNA,i,60)
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}
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/^c annot/ {
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genename=$3
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}
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/^c begin_entry/ {
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Cds = ""
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Iexon = 0
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next
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}
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/^e exon/ {
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RevStrand = ($6 == "-")
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if (++Iexon == 1) { # first is exon with start (even on - strand)
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Modif = $15
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gsub("\"", "", Modif)
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Modif = (RevStrand ? substr(Modif, 2, 1) : substr(Modif, 1, 1))
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}
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if (RevStrand)
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Cds = SubSeq(Seq, $3, $4) "" Cds
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else
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Cds = Cds "" SubSeq(Seq, $3, $4)
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next
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}
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