Eric Coissac
37e1ecc9fd
Former-commit-id: 77fd69c9687bfc7cfd3305299c7c81d2a9eddada Former-commit-id: 4d09933673c30d6a9b2b9cc985b33ef23d7a99f4
118 lines
2.4 KiB
Bash
118 lines
2.4 KiB
Bash
#
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# Bash file to be sourced at the begining of each bash script
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# for setting up basic variables and functions
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#
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########################
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#
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# General usage functions
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#
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#
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function getAbsolutePath {
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[[ -d $1 ]] && { cd "$1"; echo "$(pwd -P)"; } ||
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{ cd "$(dirname "$1")"; echo "$(pwd -P)/$(basename "$1")"; }
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}
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# Manage temp directory
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function pushTmpDir {
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TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
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pushd $TMP_DIR >& /dev/null
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}
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function popTmpDir {
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popd >& /dev/null
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rm -rf $TMP_DIR >& /dev/null
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}
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# Logging functions
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function errcho {
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>&2 echo $*
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}
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function openLogFile {
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LOGFILE=$1
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touch ${LOGFILE}
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}
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function loginfo {
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1"
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if [[ ! -z ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1" >> ${LOGFILE}
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fi
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}
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function logerror {
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1"
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if [[ ! -z ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1" >> ${LOGFILE}
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fi
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}
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function logwarning {
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1"
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if [[ ! -z ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${LOGFILE}
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fi
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}
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# Sequence related functions
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function fastaCount {
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grep '^>' $1 | wc -l
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}
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#
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#
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########################
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########################
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#
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# Local variable definitions
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#
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#
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# The absolute path to the ORG.Annote home direcotory
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ORG_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
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ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annnote instance
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PROG_DIR="$(getAbsolutePath $(dirname $0))" # Directory containing the main script file
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DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
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CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
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IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to the
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# Inverted repeat strucuture
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#
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#
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########################
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########################
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#
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# Altering the environment
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#
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#
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# We alter the path to include the bin dir corresponding to the port
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PATH="${ORG_HOME}/ports/${ORG_PORTNAME}/bin:${PATH}"
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export PATH
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# Force to basic international setting for a correction behaviour of AWK on mac with float
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export LANG=C
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export LC_ALL=C
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