PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Add annotation of nuclear rDNA cistron

Browse Source 
Former-commit-id: ee54019ddddbea4d17956622968f6ce673b609e1
Former-commit-id: 5e5381cf59409ca3dc01098b0e3f330efe0a6a32
This commit is contained in:
Eric Coissac
2016-05-02 10:56:40 +02:00
parent 7d04371387
commit 8113b80d47
8 changed files with 72157 additions and 45 deletions
Download Patch File Download Diff File Expand all files Collapse all files

145
org-annotate.sh
View File

@ -23,9 +23,41 @@ taxid="no"
normalization="yes"
irdetection="yes"
organism="no"
types="chloro"
function usage {
echo "Usage:" ;
echo " $1 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
echo ' [-i|--no-ir-detection] [-h|--help] \ '
echo ' [-o|--organism <organism_name>] \ '
echo ' [-c|--chloroplast|-r|--nuclear-rdna|-m|--mitochondrion] <FASTAFILE>'
echo
echo "Options:"
echo ' -t ### | --ncbi-taxid ###'
echo ' ### represents the ncbi taxid associated to the sequence'
echo
echo ' -i | --no-ir-detection'
echo ' Does not look for inverted repeats in the plastid genome'
echo
echo ' -o | --organism <organism_name>'
echo ' Allows for specifiying the organism name in the embl generated file'
echo ' Spaces have to be substituted by underscore ex : Abies_alba'
echo
echo ' -c | --chloroplast'
echo ' Selects for the annotation of a chloroplast genome'
echo ' This is the default mode'
echo
echo ' -r | --nuclear-rdna'
echo ' Selects for the annotation of the rDNA nuclear cistron'
echo
echo ' -m | --mitochondrion'
echo ' Selects for the annotation of an animal mitochondrion genome'
exit $2
}
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:o:ih -l ncbi-taxid:,organism,no-ir-detection,help -- "$@")
if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
exit 1
@ -36,20 +68,13 @@ eval set -- "$options"
while [ $# -gt 0 ]
do
case $1 in
-t|--ncbi-taxid) taxid="$2" ; shift;;
-t|--ncbi-taxid) taxid="$2" ; shift ;;
-i|--no-ir-detection) irdetection="no" ;;
-o|--organism) organism="$2" ; shift;;
-h|--help) echo "Usage:" ;
echo " $0 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
echo " [-i|--no-ir-detection] [-h|--help] <FASTAFILE>"
echo
echo "Options:"
echo ' -t ### | --ncbi-taxid ###'
echo ' ### represents the ncbi taxid associated to the sequence'
echo
echo ' -i | --no-ir-detection'
echo ' Does not look for inverted repeats in the plastid genome'
exit 0;;
-o|--organism) organism="$2" ; shift ;;
-c|--chloroplast) types="chloro" ;;
-r|--nuclear-rdna) types="nucrdna" ;;
-m|--mitochondrion) types="mito" ;;
-h|--help) usage $0 0;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
(*) break;;
@ -57,6 +82,7 @@ do
shift
done
echo $type
#############################
pushTmpDir ORG.organnot
@ -73,43 +99,78 @@ pushTmpDir ORG.organnot
rm -f ${LOG}
openLogFile ${LOG}
if [ "$irdetection"=="yes" ]; then
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
case "$types" in
chloro)
loginfo "Annotating a plant chloroplast genome..."
if [ "$irdetection"=="yes" ]; then
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
fi
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
topology="circular"
defline="plastid, complete genome"
;;
nucrdna)
loginfo "Annotating a plant rDNA cistron..."
loginfo "Normalizing the structure of the cistron sequence..."
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh ${QUERY} > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
loginfo "Done."
topology="linear"
defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
;;
mito)
loginfo "Annotating an animal mitochondrial genome..."
logerror "Not yet implemented"
topology="circular"
defline="mitochondrion, complete genome"
exit 1
;;
*)
echo usage $0 1;;
esac
if [[ "${organism}" == "no" ]]; then
organism="{organism}"
else
organism="$(echo ${organism} | tr '_' ' ')"
fi
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing minimal header..."
echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "ID XXX; XXX; ${topology}; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
echo "XX"
echo "AC XXX;"
echo "DE ${organism} ${defline}."
echo "XX"
if [[ "${organism}" == "no" ]]; then
echo "DE {organism} plastid, complete genome."
else
echo "DE $(echo ${organism} | tr '_' ' ') plastid, complete genome."
fi
echo "XX"
loginfo "Done."
loginfo "Printing annotations header..."