Eric Coissac
a25ab81b38
complemented Former-commit-id: ba55f354ea7a51119fe44bcb36aa5927194293e2 Former-commit-id: dd7715be54ac92c9625f0a2c30e572b7aee76dc7
72 lines
1.9 KiB
Bash
Executable File
72 lines
1.9 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 "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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loginfo "Sequence length $(seqlength ${QUERY})"
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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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loginfo "Revert complement rDNA cluster cistron"
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fastarevcomp ${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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