Eric Coissac
f3a045f2ac
Former-commit-id: e5098910d2d5221ccd14b8f840dd12aace06b4d1 Former-commit-id: ea266ab1602753cc926822f34db668049ff193c4
43 lines
946 B
Bash
Executable File
43 lines
946 B
Bash
Executable File
#!/bin/bash
|
|
#
|
|
# Annotate tRNA
|
|
#
|
|
#========================================================================================
|
|
#
|
|
# Annotate tRNA based on the Aragorn software predictions.
|
|
#
|
|
# go_trna.sh <FASTAFILE>
|
|
#
|
|
# - <FASTAFILE> : The fasta file containing the genome to annotate
|
|
#
|
|
# Results are printed to the standart output
|
|
#
|
|
#========================================================================================
|
|
|
|
# -- CAUTION -- Works as long as the script
|
|
# is not called through a symlink
|
|
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
|
|
source "${THIS_DIR}/../../../scripts/bash_init.sh"
|
|
|
|
pushTmpDir ORG.trna
|
|
|
|
CAUTRNADB="${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
|
|
export CAUTRNADB
|
|
|
|
if [[ ! "$1" =~ ^/ ]]; then
|
|
QUERY="${CALL_DIR}/$1"
|
|
else
|
|
QUERY="$1"
|
|
fi
|
|
|
|
TRNA=$(basename ${QUERY})
|
|
|
|
aragorn -i -w -seq -gc11 ${QUERY} | \
|
|
${AwkCmd} -f ${PROG_DIR}/../lib/aragorn_wrapper.awk
|
|
|
|
|
|
popTmpDir
|
|
|
|
exit 0
|
|
|