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Adds changes to conform with EMBL template files

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Former-commit-id: 93da2c4c6fe0ca46de5adb439341e970ba5abd55
Former-commit-id: 0ba15a4167e769b8e13507bd399892eb6098b4c8
This commit is contained in:
Eric Coissac
2021-11-04 21:55:59 +01:00
parent 59a53bf482
commit 775d1a7157
2 changed files with 240 additions and 54 deletions
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37
detectors/nucrrna/bin/go_nucrrna.sh
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@ -50,7 +50,7 @@ pushTmpDir ORG.its
if [[ ${#TSU[@]}=="2" ]] ; then
echo "FT rRNA ${TSU[0]}..${TSU[1]}"
echo 'FT /gene="5.8S rRNA"'
echo 'FT /product="5.8S ribosomal nuclear RNA"'
echo 'FT /product="5.8S ribosomal RNA"'
fi
if [[ ${#ITS2[@]}=="2" ]] ; then
@ -61,23 +61,26 @@ pushTmpDir ORG.its
hmmsearch --max ${RRNADB} ${QUERY} | \
$AwkCmd '/Query: / { \
profil=$2; \
match($3,"[0-9][0-9]*");\
lprof=substr($3,RSTART,RLENGTH)} \
/ [0-9][0-9]* ! / { \
$AwkCmd '/Query: / {
profil=$2
match($3,"[0-9][0-9]*");
lprof=substr($3,RSTART,RLENGTH)}
/ [0-9][0-9]* ! / {
print profil,lprof,$7,$8,$10,$11}' | \
$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
full=1;$5=$5-$3+1;$6=$6+($2-$4)} \
{loc=$5".."$6} \
($1 ~ /_RC$/) { \
loc="complement("loc")"} \
(full==1) {match($1,"_..*S");\
rrna=substr($1,RSTART+1,RLENGTH-1);\
print "FT rRNA " loc; \
print "FT /gene=\"rrn"rrna"\""
print "FT /product=\""rrna" ribosomal RNA\"";\
full=0
$AwkCmd '($3 <=5) && (($2-$4) <=5) {
full=1;$5=$5-$3+1;$6=$6+($2-$4)
}
{ loc=$5".."$6 }
($1 ~ /_RC$/) {
loc="complement("loc")"
}
(full==1) {
match($1,"_..*S")
rrna=substr($1,RSTART+1,RLENGTH-1)
print "FT rRNA " loc
print "FT /gene=\""rrna" rRNA\""
print "FT /product=\""rrna" ribosomal RNA\""
full=0
}'
loginfo "Done."