Eric Coissac
831669433e
Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
367 lines
9.1 KiB
Bash
367 lines
9.1 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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export AwkCmd="gawk"
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# setup the LC_ALL environment variable (for Linux mostly)
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# so the GNU tools (like sort) will work properly
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export LANG=C
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export LC_ALL=C
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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 "$1")"; }
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}
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# Manage temp directory
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function mktempdir {
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local TMP_DIR
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TMP_DIR=$(mktemp -d -t "$1_proc_$$_XXXXXX")
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logdebug "Creating temp directory $TMP_DIR"
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echo $TMP_DIR
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}
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function pushTmpDir {
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local TMP_DIR
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TMP_DIR=$(mktempdir "$1")
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pushd $TMP_DIR >& /dev/null
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TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
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logdebug "Pushing temp directory $TMP_DIR"
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logdebug "Stack : ${TMP_DIR_STACK}"
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}
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function popTmpDir {
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local TMP_DIR
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TMP_DIR=$($AwkCmd '{print $1}' <<< $TMP_DIR_STACK)
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TMP_DIR_STACK=$($AwkCmd '{$1="";print $0}' <<< $TMP_DIR_STACK)
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popd >& /dev/null
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rm -rf $TMP_DIR >& /dev/null
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logdebug "Poping temp directory $TMP_DIR"
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logdebug "Stack : ${TMP_DIR_STACK}"
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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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ORG_LOGFILE=$1
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export ORG_LOGFILE
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touch ${ORG_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 ${ORG_LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1" >> ${ORG_LOGFILE}
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fi
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}
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function logerror {
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1"
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if [[ ! -z ${ORG_LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1" >> ${ORG_LOGFILE}
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fi
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}
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function logwarning {
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1"
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if [[ ! -z ${ORG_LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${ORG_LOGFILE}
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fi
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}
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function logdebug {
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if [[ ! -z ${ORG_DEBUG} ]]; then
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errcho `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG ] $$ -- $1"
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if [[ ! -z ${ORG_LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA DEBUG ] $$ -- $1" >> ${ORG_LOGFILE}
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fi
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fi
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}
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#
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# Asserts that the number of arguments passed to the script
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# is at least equal to the first argument of the function.
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#
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# needarg 3
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#
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# requires that the script is called at least with 3 arguments
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#
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__ORG_ANNOT_ARGS_SCRIPT_COUNT__=$#
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function needarg {
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if (( $__ORG_ANNOT_ARGS_SCRIPT_COUNT__ < $1 )) ; then
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logerror "not enougth arguments provided"
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exit 1
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fi
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}
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function needfile {
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if [[ ! -e $1 ]] ; then
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logerror "File $1 doesn't exist"
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exit 1
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fi
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}
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function needdir {
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if [[ ! -d $1 ]] ; then
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logerror "Directory $1 doesn't exist"
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exit 1
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fi
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}
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function assignundef {
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local value=$(eval echo \${$1+x})
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if [[ -z "$value" ]] ; then
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eval $1=$2
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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 $1 | \
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wc |\
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$AwkCmd -v t="$(head -1 $1 | wc -c)" '{print $3 - t - $1 + 1}'
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}
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function readfirstfastaseq {
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awk '(/^>/ && first) {on=0}
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(on) {seq=seq $1}
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(/^>/ && ! first) { first = 1
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on = 1
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}
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END {print seq}
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' $*
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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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# - $3 : End of the subsequence (included in the subsequence)
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function cutseq {
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$AwkCmd -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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# - $1 : The fasta file containing the sequences to join
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function joinfasta {
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$AwkCmd '(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 fasta1line {
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$AwkCmd '(/^>/ && seq !="") {print seq} \
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/^>/ {print $0;seq=""} \
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!/^>/ {seq=seq $0} \
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END {print seq}' "${1}"
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}
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function formatfasta {
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$AwkCmd '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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(seq && /^>/) { printfasta(seq); \
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seq=""} \
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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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# Reverse complement a DNA string
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# - $1 : The DNA string to reverse complement
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function reversecomp {
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echo $* \
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| tr 'Aa' '@!' | tr 'Tt' 'Aa' | tr '@!' 'Tt' \
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| tr 'Cc' '@!' | tr 'Gg' 'Cc' | tr '@!' 'Gg' \
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| tr 'Mm' '@!' | tr 'Kk' 'Mm' | tr '@!' 'Kk' \
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| tr 'Rr' '@!' | tr 'Yy' 'Rr' | tr '@!' 'Yy' \
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| tr 'Ww' '@!' | tr 'Ss' 'Ww' | tr '@!' 'Ss' \
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| tr 'Bb' '@!' | tr 'Vv' 'Bb' | tr '@!' 'Vv' \
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| tr 'Dd' '@!' | tr 'Hh' 'Dd' | tr '@!' 'Hh' \
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| rev
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}
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function annotatedParts() {
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egrep -A 3 "^FT (CDS|rRNA|tRNA)" $1 \
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| egrep -v -- '^--' \
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| egrep -v '^FT +/' \
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| egrep -o '[0-9]+\.\.[0-9]+' \
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| awk -F'.' '($1 > $3) {x=$3;$3=$1;$1=x} {print $1"-"$3}' \
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| sort -n
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}
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function notAnnoted() {
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local annotations=$1
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local genome=$2
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local genomesize=$(seqlength $genome)
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local minimum=$3
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local from=1
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for part in $(annotatedParts ${annotations}) ; do
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loc=( $(tr '-' ' ' <<< $part) )
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begin=${loc[0]}
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end=${loc[1]}
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if (( ( begin - from ) >= minimum )) ; then
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cutseq "${genome}" $from $(( begin - 1 )) \
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| $AwkCmd -v from=$from -v to=$(( begin - 1 )) '
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/^>/ {$0=$1 " from=" from "; to=" to ";"}
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{print $0}
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'
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fi
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from=$((end+1))
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done
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if (( ( genomesize - from + 1 ) >= minimum )) ; then
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cutseq "${genome}" $from $genomesize \
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| $AwkCmd -v from=$from -v to=$genomesize '
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/^>/ {$0=$1 " from=" from "; to=" to ";"}
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{print $0}
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'
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fi
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}
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#
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# Process management related function
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#
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function timeoutcmd() {
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local seconde=$1
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shift
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$* &
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local mainpid=$!
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sleep $seconde &
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local sleeppid=$!
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local nproc=$(ps $mainpid $sleeppid | tail -n +2 | wc -l)
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while (( nproc > 1 )) ; do
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sleep 1
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nproc=$(ps $mainpid $sleeppid | tail -n +2 | wc -l)
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done
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local timealive=$(ps $sleeppid | tail -n +2 | wc -l)
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if (( timealive > 0 )) ; then
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kill -9 $sleeppid
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else
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if (( $(ps $mainpid | tail -n +2 | wc -l) > 0 )) ; then
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kill -9 $mainpid
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logwarning "Timeout after ${seconde}s on command : $*"
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return 1
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fi
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fi
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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.Annot home directory
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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.Annot instance
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BIN_DIR="${ORG_HOME}/ports/${ORG_PORTNAME}/bin" # Directory containing binaries for this port
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SCRIPT_DIR="${ORG_HOME}/scripts" # Directory containing scripts utilities
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PROG_DIR="$(getAbsolutePath $(dirname $0))" # Directory containing the main script file
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LIB_DIR="$(getAbsolutePath ${PROG_DIR}/../lib)" # Directory containing the main script libraries
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CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
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DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
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IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to
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# IRs detection
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TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
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# tRNAs detection
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CDS_DATA_DIR="${DATA_DIR}/cds" # Directory containing data related to
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# CDSs detection
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RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
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# rRNAs detection
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NUCRRNA_DATA_DIR="${DATA_DIR}/nucrrna" # Directory containing data related to
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# rRNAs detection
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ITS_DATA_DIR="${DATA_DIR}/its" # Directory containing data related to
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# rRNAs detection
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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="${SCRIPT_DIR}:${BIN_DIR}:${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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