Eric Coissac
8b27f23a8e
Former-commit-id: fa0b02e712db163ba6d37407cea46d1d413a7cb5 Former-commit-id: f393558b7962188159ac123d654ae14ee581f5f8
43 lines
940 B
Bash
Executable File
43 lines
940 B
Bash
Executable File
#!/bin/bash
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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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#
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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 as 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.trna
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CAUTRNADB="${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
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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="$1"
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fi
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TRNA=$(basename ${QUERY})
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aragorn -i -w -seq ${QUERY} | \
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${AwkCmd} -f ${PROG_DIR}/../lib/aragorn_wrapper.awk
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popTmpDir
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exit 0
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