Eric Coissac
921682f75a
Former-commit-id: 0669e643dea2391c8370246cd3182b6328c068dc Former-commit-id: 7820b800405b2134f2f0c2e27c4ef1ec73e1dc0d
58 lines
1.6 KiB
Bash
Executable File
58 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
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#
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# Annotate rRNA
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#
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#========================================================================================
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#
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# Annotate rRNA genes based on HMMER3 profils.
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#
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# go_rrna.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome 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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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.rrna
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RRNADB="${RRNA_DATA_DIR}/plast_RRNA.hmm"
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export CAUTRNADB
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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="$1"
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fi
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RRNA=$(basename ${QUERY})
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hmmsearch --max ${RRNADB} ${QUERY} | \
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awk '/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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awk '($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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popTmpDir
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exit 0
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