Eric Coissac
5a7b869170
Former-commit-id: 878d919fdaad16e6e2645b62b3a53ef5d5e1ef2b Former-commit-id: 3c3647cf114438a1ea9c3ff8c44e67e367929776
63 lines
1.2 KiB
Awk
63 lines
1.2 KiB
Awk
#
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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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Prot = Translate(substr(Cds, 1, length(Cds)-3),Modif,"chloroplast")
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if (Modif == "=" && substr(Prot, 1,1) != "M") {
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Prot = "M" substr(Prot, 2,length(Prot))
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if (CdsStartPosFull==1) {
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print "e trans_exception "CdsStartPos" Met"
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} else {
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print "e trans_exception " "ERROR" " Met"
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}
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}
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print "e translate " Prot
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}
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{
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print $0
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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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CdsStartPosFullv = 0
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next
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}
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/^e exon/ {
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print "d cds " CDS
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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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if (Iexon==1) {
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if(($4 - $3 +1) >= 3) {
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CdsStartPos="complement("$4-2".."$4")"
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CdsStartPosFull=1
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}
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}}
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else{
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Cds = Cds "" SubSeq(Seq, $3, $4)
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if (Iexon==1) {
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if (Iexon==1) {
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if(($4 - $3 +1) >= 3) {
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CdsStartPos=$3".."$3+2
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CdsStartPosFull=1
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}
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}
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} }
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next
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}
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