Add annotation of nuclear rDNA cistron
Former-commit-id: ee54019ddddbea4d17956622968f6ce673b609e1 Former-commit-id: 5e5381cf59409ca3dc01098b0e3f330efe0a6a32
This commit is contained in:
29834
data/nucrrna/plants/nuc_RRNA.hmm
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29834
data/nucrrna/plants/nuc_RRNA.hmm
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1440
data/nucrrna/plants/nuc_RRNA_18S.fst
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1440
data/nucrrna/plants/nuc_RRNA_18S.fst
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File diff suppressed because it is too large
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40600
data/nucrrna/plants/nuc_RRNA_28S.fst
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40600
data/nucrrna/plants/nuc_RRNA_28S.fst
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70
detectors/normalizerdna/bin/go_normalizerdna.sh
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70
detectors/normalizerdna/bin/go_normalizerdna.sh
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@ -0,0 +1,70 @@
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#!/bin/bash
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#
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# Annotate the Intergenic Spacer (ITS) of nuclear rDNA cluster
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#
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#========================================================================================
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#
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# This script is based on ITSx
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#
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#
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# go_its.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the cluster to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.its
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loginfo "Normalizing nuclear rDNA cistron..."
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RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm"
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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strand=( $(hmmsearch --max ${RRNADB} ${QUERY} | \
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$AwkCmd '/Query: / { \
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profil=$2; \
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match($3,"[0-9][0-9]*");\
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lprof=substr($3,RSTART,RLENGTH)} \
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/ [0-9][0-9]* ! / { \
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print profil,lprof,$7,$8,$10,$11}' | \
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$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
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full=1;$5=$5-$3+1;$6=$6+($2-$4)} \
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{loc="Forward"} \
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($1 ~ /_RC$/) { \
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loc="Reverse"} \
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(full==1) {match($1,"_..*S");\
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rrna=substr($1,RSTART+1,RLENGTH-1);\
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print loc;\
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full=0
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}' | sort | uniq) )
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if [[ "${#strand[@]}" == 1 ]] ; then
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if [[ "${strand[0]}" == "Forward" ]] ; then
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cat ${QUERY}
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else
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fastarevcomp -f ${QUERY}
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fi
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else
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logerror "Cannot determine the Cistron orientation"
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exit 1
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fi
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loginfo "Done."
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popTmpDir
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exit 0
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88
detectors/nucrrna/bin/go_nucrrna.sh
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detectors/nucrrna/bin/go_nucrrna.sh
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@ -0,0 +1,88 @@
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#!/bin/bash
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#
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# Annotate the Intergenic Spacer (ITS) of nuclear rDNA cluster
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#
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#========================================================================================
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#
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# This script is based on ITSx
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#
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#
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# go_its.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the cluster to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.its
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loginfo "Annotating ITS and TSU..."
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RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm"
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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ITSx -p "${ITS_DATA_DIR}/ITSx_db/HMMs" -i "${QUERY}" -o "output.itsx"
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ITS1=( $(sed -E 's/.*ITS1: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
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ITS2=( $(sed -E 's/.*ITS2: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
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TSU=( $(sed -E 's/.*5\.8S: *([0-9]+)-([0-9]+).*/\1 \2/' "output.itsx.positions.txt" ) )
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if [[ ${#ITS1[@]}=="2" ]] ; then
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echo "FT misc_RNA ${ITS1[0]}..${ITS1[1]}"
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echo 'FT /gene="ITS1"'
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echo 'FT /note="internal transcribed spacer 1, ITS1"'
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fi
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if [[ ${#TSU[@]}=="2" ]] ; then
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echo "FT rRNA ${TSU[0]}..${TSU[1]}"
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echo 'FT /gene="5.8S rRNA"'
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echo 'FT /product="5.8S ribosomal nuclear RNA"'
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fi
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if [[ ${#ITS2[@]}=="2" ]] ; then
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echo "FT misc_RNA ${ITS2[0]}..${ITS2[1]}"
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echo 'FT /gene="ITS2"'
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echo 'FT /note="internal transcribed spacer 2, ITS2"'
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fi
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hmmsearch --max ${RRNADB} ${QUERY} | \
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$AwkCmd '/Query: / { \
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profil=$2; \
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match($3,"[0-9][0-9]*");\
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lprof=substr($3,RSTART,RLENGTH)} \
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/ [0-9][0-9]* ! / { \
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print profil,lprof,$7,$8,$10,$11}' | \
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$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
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full=1;$5=$5-$3+1;$6=$6+($2-$4)} \
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{loc=$5".."$6} \
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($1 ~ /_RC$/) { \
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loc="complement("loc")"} \
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(full==1) {match($1,"_..*S");\
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rrna=substr($1,RSTART+1,RLENGTH-1);\
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print "FT rRNA " loc; \
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print "FT /gene=\"rrn"rrna"\""
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print "FT /product=\""rrna" ribosomal RNA\"";\
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full=0
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}'
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loginfo "Done."
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popTmpDir
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exit 0
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145
org-annotate.sh
145
org-annotate.sh
@ -23,9 +23,41 @@ taxid="no"
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normalization="yes"
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irdetection="yes"
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organism="no"
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types="chloro"
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function usage {
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echo "Usage:" ;
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echo " $1 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
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echo ' [-i|--no-ir-detection] [-h|--help] \ '
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echo ' [-o|--organism <organism_name>] \ '
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echo ' [-c|--chloroplast|-r|--nuclear-rdna|-m|--mitochondrion] <FASTAFILE>'
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echo
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echo "Options:"
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echo ' -t ### | --ncbi-taxid ###'
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echo ' ### represents the ncbi taxid associated to the sequence'
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echo
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echo ' -i | --no-ir-detection'
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echo ' Does not look for inverted repeats in the plastid genome'
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echo
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echo ' -o | --organism <organism_name>'
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echo ' Allows for specifiying the organism name in the embl generated file'
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echo ' Spaces have to be substituted by underscore ex : Abies_alba'
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echo
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echo ' -c | --chloroplast'
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echo ' Selects for the annotation of a chloroplast genome'
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echo ' This is the default mode'
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echo
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echo ' -r | --nuclear-rdna'
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echo ' Selects for the annotation of the rDNA nuclear cistron'
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echo
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echo ' -m | --mitochondrion'
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echo ' Selects for the annotation of an animal mitochondrion genome'
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exit $2
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}
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# options may be followed by one colon to indicate they have a required argument
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if ! options=$(getopt -o t:o:ih -l ncbi-taxid:,organism,no-ir-detection,help -- "$@")
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if ! options=$(getopt -o t:o:icrmh -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,help -- "$@")
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then
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# something went wrong, getopt will put out an error message for us
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exit 1
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@ -36,20 +68,13 @@ eval set -- "$options"
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while [ $# -gt 0 ]
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do
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case $1 in
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-t|--ncbi-taxid) taxid="$2" ; shift;;
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-t|--ncbi-taxid) taxid="$2" ; shift ;;
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-i|--no-ir-detection) irdetection="no" ;;
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-o|--organism) organism="$2" ; shift;;
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-h|--help) echo "Usage:" ;
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echo " $0 "'[-t|--ncbi-taxid ###] [-n|--no-normalization] \'
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echo " [-i|--no-ir-detection] [-h|--help] <FASTAFILE>"
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echo
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echo "Options:"
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echo ' -t ### | --ncbi-taxid ###'
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echo ' ### represents the ncbi taxid associated to the sequence'
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echo
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echo ' -i | --no-ir-detection'
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echo ' Does not look for inverted repeats in the plastid genome'
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exit 0;;
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-o|--organism) organism="$2" ; shift ;;
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-c|--chloroplast) types="chloro" ;;
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-r|--nuclear-rdna) types="nucrdna" ;;
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-m|--mitochondrion) types="mito" ;;
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-h|--help) usage $0 0;;
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(--) shift; break;;
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(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
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(*) break;;
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@ -57,6 +82,7 @@ do
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shift
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done
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echo $type
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#############################
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pushTmpDir ORG.organnot
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@ -73,43 +99,78 @@ pushTmpDir ORG.organnot
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rm -f ${LOG}
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openLogFile ${LOG}
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if [ "$irdetection"=="yes" ]; then
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loginfo "Normalizing the structure of the Chloroplast sequence..."
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loginfo " LSC + IRB + SSC + IRA"
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
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loginfo "Done."
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case "$types" in
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chloro)
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loginfo "Annotating a plant chloroplast genome..."
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if [ "$irdetection"=="yes" ]; then
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loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
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${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Normalizing the structure of the Chloroplast sequence..."
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loginfo " LSC + IRB + SSC + IRA"
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
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loginfo "Done."
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loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
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${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
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loginfo "Done."
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fi
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loginfo "Annotating the tRNA..."
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${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the rRNA genes..."
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${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the CDS..."
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tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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topology="circular"
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defline="plastid, complete genome"
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;;
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nucrdna)
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loginfo "Annotating a plant rDNA cistron..."
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loginfo "Normalizing the structure of the cistron sequence..."
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${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh ${QUERY} > "${RESULTS}.norm.fasta"
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loginfo "Done."
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loginfo "Annotating the rRNA genes..."
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${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
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loginfo "Done."
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topology="linear"
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defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
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;;
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mito)
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loginfo "Annotating an animal mitochondrial genome..."
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logerror "Not yet implemented"
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topology="circular"
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defline="mitochondrion, complete genome"
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exit 1
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;;
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*)
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echo usage $0 1;;
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esac
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if [[ "${organism}" == "no" ]]; then
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organism="{organism}"
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else
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organism="$(echo ${organism} | tr '_' ' ')"
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fi
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loginfo "Annotating the tRNA..."
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${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the rRNA genes..."
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${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the CDS..."
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tcsh -f ${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Printing minimal header..."
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echo "ID XXX; XXX; circular; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
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echo "ID XXX; XXX; ${topology}; genomic DNA; XXX; XXX; $(seqlength ${RESULTS}.norm.fasta) BP."
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echo "XX"
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echo "AC XXX;"
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echo "DE ${organism} ${defline}."
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echo "XX"
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if [[ "${organism}" == "no" ]]; then
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echo "DE {organism} plastid, complete genome."
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else
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echo "DE $(echo ${organism} | tr '_' ' ') plastid, complete genome."
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fi
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echo "XX"
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loginfo "Done."
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loginfo "Printing annotations header..."
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@ -182,6 +182,12 @@ CDS_DATA_DIR="${DATA_DIR}/cds" # Directory containing data related to
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RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
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# rRNAs detection
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NUCRRNA_DATA_DIR="${DATA_DIR}/nucrrna" # Directory containing data related to
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# rRNAs detection
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ITS_DATA_DIR="${DATA_DIR}/its" # Directory containing data related to
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# rRNAs detection
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#
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#
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@ -25,31 +25,44 @@ PRTPATH = $(abspath $(PRTDIR))
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DATADIR = $(CFGDIR)../data
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DATAITS = $(DATADIR)/its
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HMMPRESS= $(BINDIR)/hmmpress
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HMMDIR = $(PKGDIR)/ITSx_db/HMMs
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HMMS = $(wildcard $(HMMDIR)/*.hmm)
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HMMP = $(patsubst %.hmm,%.hmm.h3p,$(HMMS))
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HMMI = $(patsubst %.hmm,%.hmm.h3i,$(HMMS))
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HMMM = $(patsubst %.hmm,%.hmm.h3m,$(HMMS))
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#
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# Rules
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#
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.PHONY: all clean test portclean pkg pkg.expand pkg.install
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all:: pkg
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%.hmm.h3i: %.hmm
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echo $(HMMPRESS)
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(! test -s $< ) || $(HMMPRESS) -f $<
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all:: pkg.install
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pkg.expand::
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test -d $(PKGDIR) || mkdir $(PKGDIR)
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$(TAR) zxf $(PKGTAR) -C $(PKGDIR) --strip-components 1
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pkg.install:: pkg.expand
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pkg.install:: pkg
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@mkdir -p $(BINDIR)
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@cp $(PKGDIR)/ITSx $(BINDIR)
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@mkdir -p $(DATAITS)
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@cp -r $(PKGDIR)/ITSx_db $(DATAITS)
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@echo "+++++++++++ package $(PKG) done"
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pkg:: pkg.install
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pkg:: pkg.expand clean $(HMMI)
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test::
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echo No test available
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clean::
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\rm -f $(HMMP) $(HMMI) $(HMMM)
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echo Done
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portclean::
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