Eric Coissac
8113b80d47
Former-commit-id: ee54019ddddbea4d17956622968f6ce673b609e1 Former-commit-id: 5e5381cf59409ca3dc01098b0e3f330efe0a6a32
89 lines
2.6 KiB
Bash
Executable File
89 lines
2.6 KiB
Bash
Executable File
#!/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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