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Remove extra feature for CDS

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Former-commit-id: 19b149eb57227e4ff3e7dda97f0328207fbc6373
Former-commit-id: ef94884d026004aa80d0fed85121c525cf5610b4
This commit is contained in:
Eric Coissac
2022-02-14 15:09:17 +01:00
parent 1d18a6f720
commit d56aeaf698
2 changed files with 17 additions and 17 deletions
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4
detectors/cds/bin/do_rps12.sh
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@ -264,9 +264,9 @@ blastx \
export PASS1_SPEEDUP=0 export PASS1_SPEEDUP=0
cp $DBROOT/Annot.lst RPS12 cp $DBROOT/Annot.lst RPS12
for f in rps12_fragments_*.fasta ; do for fasta in rps12_fragments_*.fasta ; do
tcsh -f ${PROG_DIR}/do_exonerate.csh \ tcsh -f ${PROG_DIR}/do_exonerate.csh \
$f \ $fasta \
"RPS12/rps12.fasta" \ "RPS12/rps12.fasta" \
$DBROOT/../models $(pwd) $DBROOT/../models $(pwd)
done done

30
detectors/cds/lib/toEmbl.awk
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@ -191,23 +191,23 @@ function Unk(s) {
} }
if (Nexon > 1) { # if (Nexon > 1) {
for (i = 1 ; i <= Nexon ; i++) { # for (i = 1 ; i <= Nexon ; i++) {
Feature("exon", ExonLocation(i)) # Feature("exon", ExonLocation(i))
QQualifier("gene", gname) # QQualifier("gene", gname)
QQualifier("locus_tag", locus) # QQualifier("locus_tag", locus)
if (Exon[i]["frameshift"]) { # if (Exon[i]["frameshift"]) {
QQualifier("pseudogene","unknown") # QQualifier("pseudogene","unknown")
if (Exon[i]["frameshift"] > 0) # if (Exon[i]["frameshift"] > 0)
QQualifier("note","frameshifted by insertion of " Exon[i]["frameshift"] " bp") # QQualifier("note","frameshifted by insertion of " Exon[i]["frameshift"] " bp")
else # else
QQualifier("note","frameshifted by deletion of " -Exon[i]["frameshift"] " bp") # QQualifier("note","frameshifted by deletion of " -Exon[i]["frameshift"] " bp")
} # }
SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1) # SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1)
} # }
} # }
} }