Commit f71b0396 by Eric Coissac

Add missing file...

parent aeae3d48
#
# translate CDSs from iff file
#
BEGIN {
Seq = ReadFasta(FASTA)
}
/^c end_entry/ {
if (RevStrand) Cds = RevComplement(Cds)
DNA = substr(Cds, 1, length(Cds)-3)
print ">" genename
for (i=1; i<=length(DNA); i+=60)
print substr(DNA,i,60)
}
/^c annot/ {
genename=$3
}
/^c begin_entry/ {
Cds = ""
Iexon = 0
next
}
/^e exon/ {
RevStrand = ($6 == "-")
if (++Iexon == 1) { # first is exon with start (even on - strand)
Modif = $15
gsub("\"", "", Modif)
Modif = (RevStrand ? substr(Modif, 2, 1) : substr(Modif, 1, 1))
}
if (RevStrand)
Cds = SubSeq(Seq, $3, $4) "" Cds
else
Cds = Cds "" SubSeq(Seq, $3, $4)
next
}
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