PhyloSkims/annotate
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change tRNA and CDS annotations

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Former-commit-id: 12b6c5605f57940e215643b80c93ffbb48d5406e
Former-commit-id: 18663d59e90e6d35b029d9087b66723487b8db1d
This commit is contained in:
Eric Coissac
2021-11-05 09:29:57 +01:00
parent 27c02dfc1b
commit 616d5d084b
3 changed files with 8 additions and 8 deletions
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2
detectors/cds/bin/do_rps12.sh
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@ -371,7 +371,7 @@ blastx \
n = split($0,parts,",") n = split($0,parts,",")
j = 1 j = 1
for (i = 1; i <= n; i++) { for (i = 1; i <= n; i++) {
if (length(line) + length(parts[i]) > 79) { if (length(line) + length(parts[i]) > 78) {
print line "," print line ","
line = "FT " line = "FT "
j = i j = i

12
detectors/cds/lib/toEmbl.awk
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@ -160,11 +160,11 @@ function Unk(s) {
gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene) gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
locus = "" locus = ""
Feature("gene", GeneLocation()) # Feature("gene", GeneLocation())
QQualifier("gene", gname) #QQualifier("gene", gname)
QQualifier("locus_tag", locus) #QQualifier("locus_tag", locus)
if (FrameShift) #if (FrameShift)
QQualifier("pseudogene","unknown") # QQualifier("pseudogene","unknown")
Feature("CDS", CdsLocation()) Feature("CDS", CdsLocation())
SQualifier("codon_start", 1) SQualifier("codon_start", 1)
@ -180,7 +180,7 @@ function Unk(s) {
} }
QQualifier("product", Product) QQualifier("product", Product)
QQualifier("inference", "similar to DNA sequence:" Simil) QQualifier("inference", "similar to DNA sequence:" Simil)
QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo) # QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
if (FrameShift==0) { if (FrameShift==0) {
if (match(Translat,/\*/)>0) { if (match(Translat,/\*/)>0) {
QQualifier("pseudogene","unknown") QQualifier("pseudogene","unknown")

2
detectors/trna/lib/aragorn_wrapper.awk
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@ -168,7 +168,7 @@ function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
print "FT /gene=\""trna"\""; print "FT /gene=\""trna"\"";
print "FT /anticodon=\""anti"\""; print "FT /anticodon=\""anti"\"";
print "FT /product=\""product"("anti")\""; print "FT /product=\""product"("anti")\"";
print "FT /inference=\"Aragorn-1.2.38\""; # print "FT /inference=\"Aragorn-1.2.38\"";
if (notes!="-") if (notes!="-")
print "FT /note=\""notes"\""; print "FT /note=\""notes"\"";