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debug intron location, update the anticondon qualifier structure to fit new model

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Former-commit-id: e5098910d2d5221ccd14b8f840dd12aace06b4d1
Former-commit-id: ea266ab1602753cc926822f34db668049ff193c4
This commit is contained in:
Eric Coissac
2023-04-29 07:09:13 +02:00
parent 06f36ccdd3
commit f3a045f2ac
2 changed files with 65 additions and 17 deletions
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2
detectors/trna/bin/go_trna.sh
View File

@ -32,7 +32,7 @@ pushTmpDir ORG.trna
TRNA=$(basename ${QUERY})
aragorn -i -w -seq -gcbact ${QUERY} | \
aragorn -i -w -seq -gc11 ${QUERY} | \
${AwkCmd} -f ${PROG_DIR}/../lib/aragorn_wrapper.awk

76
detectors/trna/lib/aragorn_wrapper.awk
View File

@ -120,10 +120,24 @@ function patchtRNA(anticodon,trna,seq) {
}
function gene2product(gene) {
return "tRNA-" AA3[substr(gene,4,1)];
return "RNA-" AA3[substr(gene,4,1)];
}
function gene2aa(gene,anticodon) {
aa1=substr(gene,4,1)
if (aa1=="f") aa1="M"
if (aa1=="I" && anticodon=="CAU") aa1="M"
return AA3[aa1];
}
function emblTRNA(geneid,trna,loc,anti,antip,intron,notes,seq) {
if (intron!="") {
l=length(intron);
intron=substr(intron,2,l-2);
split(intron,intronpos,",");
}
function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
if (loc ~ /^c/) {
complement=1;
match(loc,",[0-9][0-9]*\\]");
@ -132,21 +146,54 @@ function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
ge=substr(ge,RSTART,RLENGTH);
sub("c\\[","complement(",loc);
sub("\\]",")",loc);
sub(",","..",loc)}
sub(",","..",loc)
antistart=ge - antip + 1
antiloc="complement(" antistart - 2 ".." antistart ")"
if (intron!="") {
delta = intronpos[1] - antip - 1
if (delta==1 || delta==2) {
start= ge - (intronpos[1] + intronpos[2] -1) - 2 + delta
end= ge - (intronpos[1] + intronpos[2] -1)
if (start!=end) antie1=start".."end; else antie1=start
start= ge - intronpos[1] + 2
end=start + delta - 1
if (start!=end) antie2=start".."end; else antie2=start
antiloc="complement(join("antie1","antie2"))"
}
}
}
else {
complement=0;
sub("\\[","",loc);
sub("\\]","",loc);
sub(",","..",loc)}
split(loc,locparts,",")
sub(",","..",loc)
split(loc,locparts,",")
sub(",","..",loc)
antistart=locparts[1]+antip-1
antiloc=antistart".."(antistart+2)
if (intron!="") {
delta = intronpos[1] - antip
# print delta, intronpos[1], intronpos[2], antip,ge
if (delta == 1 || delta == 2) {
start=antistart
end=antistart + delta - 1
if (start!=end) antie1=start".."end; else antie1=start
start=locparts[1] + ( intronpos[1] + intronpos[2] - 1)
end=start + 2 - delta
if (start!=end) antie2=start".."end; else antie2=start
antiloc="join("antie1","antie2")"
}
}
}
anti=toupper(anti);
gsub("T","U",anti);
product=gene2product(trna);
aa=gene2aa(trna,anti)
if (intron!="") {
l=length(intron);
intron=substr(intron,2,l-2);
split(intron,intronpos,",");
ib=intronpos[1];
il=intronpos[2];
ie=ib+il-1;
@ -156,19 +203,20 @@ function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
sub("\\.\\.",".." (gb + ib - 2) "," (gb + ie) "..",loc);
}
else {
sub("\\.\\.",".." (ge - ie - 1) "," (ge - ib + 2) "..",loc);
sub("\\.\\.",".." (ge - ie) "," (ge - ib + 2) "..",loc);
}
sub("complement","complement(join",loc);\
if (substr(loc,1,1) ~ /[0-9]/) {
loc="join("loc}
loc=loc")";
}
print "FT tRNA " loc;
print "FT /gene=\""trna"\"";
print "FT /anticodon=\""anti"\"";
print "FT /gene=\"t" product "(" anti ")\"";
print "FT /anticodon=(pos:" antiloc ",aa:" aa ",seq:" tolower(anti) ")";
# print "FT /note=\"*anticodon: "anti"\"";
print "FT /product=\""product"("anti")\"";
print "FT /product=\"transfer " product "(" anti ")\"";
print "FT /locus_tag=\"\"";
# print "FT /inference=\"Aragorn-1.2.38\"";
if (notes!="-")
@ -285,7 +333,7 @@ BEGIN {
split(xxx,trnadata,"@");
# print geneid,trna,loc,anti,"'"intron"'",seq;
emblTRNA(geneid,trnadata[1],loc,anti,intron,trnadata[2],seq);
emblTRNA(geneid,trnadata[1],loc,anti,antip,intron,trnadata[2],seq);
seq=""
}
@ -294,7 +342,7 @@ BEGIN {
{ geneid=$1;
trna =$2;
loc =$3;
lseq =$4;
antip =$4;
x=$5;
split($5,intron_desc,"i");
anti =substr(intron_desc[1],2,3);
@ -312,5 +360,5 @@ END { seq=epissage(intron,seq);
split(xxx,trnadata,"@");
# print geneid,trna,loc,anti,"'"intron"'",seq;
emblTRNA(geneid,trnadata[1],loc,anti,intron,trnadata[2],seq);
emblTRNA(geneid,trnadata[1],loc,anti,antip,intron,trnadata[2],seq);
}