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Patch a bug on the generation of the location of tRNA for gene on

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reverse complement strand with an intron.

Former-commit-id: 729905450d60c9b2e76ac73567b3efb09cb1bb86
Former-commit-id: 722dc77682ef3da8a746879c52072c46adb9de71
This commit is contained in:
Eric Coissac
2015-11-28 16:11:14 +01:00
parent b7282fb30d
commit 89c4f17fc4
1 changed files with 14 additions and 3 deletions
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17
detectors/trna/lib/aragorn_wrapper.awk
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@ -89,10 +89,16 @@ function gene2product(gene) {
function emblTRNA(geneid,trna,loc,anti,intron,seq) { function emblTRNA(geneid,trna,loc,anti,intron,seq) {
if (loc ~ /^c/) { if (loc ~ /^c/) {
complement=1;
match(loc,",[0-9][0-9]*\\]");
ge=substr(loc,RSTART,RLENGTH);
match(ge,"[0-9][0-9]*");
ge=substr(ge,RSTART,RLENGTH);
sub("c\\[","complement(",loc); sub("c\\[","complement(",loc);
sub("\\]",")",loc); sub("\\]",")",loc);
sub(",","..",loc)} sub(",","..",loc)}
else { else {
complement=0;
sub("\\[","",loc); sub("\\[","",loc);
sub("\\]","",loc); sub("\\]","",loc);
sub(",","..",loc)} sub(",","..",loc)}
@ -105,11 +111,16 @@ function emblTRNA(geneid,trna,loc,anti,intron,seq) {
l=length(intron); l=length(intron);
intron=substr(intron,2,l-2); intron=substr(intron,2,l-2);
split(intron,intronpos,","); split(intron,intronpos,",");
ib=intronpos[0]; ib=intronpos[1];
ie=intronpos[1]; ie=intronpos[2];
match(loc,"[0-9][0-9]*"); match(loc,"[0-9][0-9]*");
gb=substr(loc,RSTART,RLENGTH); gb=substr(loc,RSTART,RLENGTH);
sub("\\.\\.",".." (gb + ib -2) "," (gb + ie) "..",loc); \ if (complement==0) {
sub("\\.\\.",".." (gb + ib - 2) "," (gb + ie) "..",loc);
}
else {
sub("\\.\\.",".." (ge - ie - 1) "," (ge - ib + 2) "..",loc);
}
sub("complement","complement(join",loc);\ sub("complement","complement(join",loc);\
if (substr(loc,1,1) ~ /[0-9]/) { if (substr(loc,1,1) ~ /[0-9]/) {
loc="join("loc} loc="join("loc}