48 lines
1.1 KiB
Bash
48 lines
1.1 KiB
Bash
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#!/bin/bash
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#
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#
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#
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# Annotate tRNA
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#
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#========================================================================================
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#
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# Annotate tRNA based on the Aragorn software predictions.
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# go_trna.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.organnot
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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="$1"
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fi
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RESULTS=$(basename ${QUERY/.*/})
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LOG="${CALL_DIR}/${RESULTS}.log"
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rm -f ${LOG}
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openLogFile ${LOG}
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
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${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
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${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
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cat "${RESULTS}.annot"
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popTmpDir
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