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First version of the tRNA detector and of the global organnot.sh script

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Former-commit-id: f2a75cf99b24875c90c426c2afb22a75b972bf60
Former-commit-id: 65e3dfb35df06ca69bb29b690c9a40e8940ac6bf
This commit is contained in:
Eric Coissac
2015-10-11 10:39:59 -03:00
parent 6015339839
commit c32f7cdde6
9 changed files with 175 additions and 133 deletions
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33
scripts/bash_init.sh
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@ -19,11 +19,18 @@ function getAbsolutePath {
function pushTmpDir {
TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
pushd $TMP_DIR >& /dev/null
TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
logdebug "Pushing temp directory $TMP_DIR"
logdebug "Stack : ${TMP_DIR_STACK}"
}
function popTmpDir {
TMP_DIR=$(echo $TMP_DIR_STACK | awk '{print $1}')
TMP_DIR_STACK=$(echo $TMP_DIR_STACK | awk '{$1="";print $0}')
popd >& /dev/null
rm -rf $TMP_DIR >& /dev/null
logdebug "Poping temp directory $TMP_DIR"
logdebug "Stack : ${TMP_DIR_STACK}"
}
# Logging functions
@ -34,32 +41,42 @@ function errcho {
}
function openLogFile {
LOGFILE=$1
touch ${LOGFILE}
ORG_LOGFILE=$1
export ORG_LOGFILE
touch ${ORG_LOGFILE}
}
function loginfo {
errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1"
if [[ ! -z ${LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1" >> ${LOGFILE}
if [[ ! -z ${ORG_LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1" >> ${ORG_LOGFILE}
fi
}
function logerror {
errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1"
if [[ ! -z ${LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1" >> ${LOGFILE}
if [[ ! -z ${ORG_LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1" >> ${ORG_LOGFILE}
fi
}
function logwarning {
errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1"
if [[ ! -z ${LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${LOGFILE}
if [[ ! -z ${ORG_LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${ORG_LOGFILE}
fi
}
function logdebug {
if [[ ! -z ${ORG_DEBUG} ]]; then
errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG ] $$ -- $1"
if [[ ! -z ${ORG_LOGFILE} ]]; then
echo `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG ] $$ -- $1" >> ${ORG_LOGFILE}
fi
fi
}
# Sequence related functions
# Counts how many sequences are stored in a fasta file