Eric Coissac
9973d1cf71
Former-commit-id: 78c4a4d8497e6dc7185a6e5726ffc643d9ea914d Former-commit-id: e6945818dbdbabd9cd060edb9d2578ea26671209
167 lines
4.0 KiB
Bash
167 lines
4.0 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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# Counts how many sequences are stored in a fasta file
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# - $1 : The fasta file to count
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function fastaCount {
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grep '^>' $1 | wc -l
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}
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# compute the sequence length from a fasta sequence
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# - $1 : The fasta file to cut
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function seqlength {
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cat $1 | \
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wc |\
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awk -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
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}
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# extract a subseq from a fasta sequence
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# - $1 : The fasta file to cut
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# - $2 : First position of the subsequence (first position is numered 1),
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# - $3 : End of the subsequence (included in the subsequence)
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function cutseq {
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awk -v from=$2 -v end=$3 'function printfasta(seq) { \
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seqlen=length(seq); \
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for (i=1; i <= seqlen; i+=60) \
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print substr(seq,i,60); \
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} \
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\
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/^>/ {print $0} \
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! /^>/ {seq=seq$0} \
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END {printfasta(substr(seq,from,end-from+1))}' $1
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}
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# Joins a set of sequences stored in a fasta file into
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# a single sequence
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# - $1 : The fasta file containing the sequences to join
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function joinfasta {
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awk '(NR==1 && /^>/) {print $0} \
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! /^>/ {print $0}' $1 | \
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formatfasta
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}
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function formatfasta {
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awk 'function printfasta(seq) { \
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seqlen=length(seq); \
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for (i=1; i <= seqlen; i+=60) \
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print substr(seq,i,60); \
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} \
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/^>/ { print $0 } \
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! /^>/ { seq=seq $0 } \
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END { printfasta(seq)}' $1
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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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