First version of the tRNA detector and of the global organnot.sh script
Former-commit-id: f2a75cf99b24875c90c426c2afb22a75b972bf60 Former-commit-id: 65e3dfb35df06ca69bb29b690c9a40e8940ac6bf
This commit is contained in:
@ -1,96 +0,0 @@
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#!/bin/bash
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#
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#
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export ORGANNOT_HOME=`dirname $0`
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REPSEEK=${ORGANNOT_HOME}/repseek
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SUMATRA=${ORGANNOT_HOME}/sumatra
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ARAGORN=${ORGANNOT_HOME}/aragorn
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WRAPARAGORN=${ORGANNOT_HOME}/aragorn_wrapper.awk
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ECOFIND=${ORGANNOT_HOME}/ecofind
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function annotateCAU {
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QUERY="$$.query.fasta"
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echo $1 | sed 's/&/ /' | tr '@' '\n' > ${QUERY}
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${SUMATRA} -d -n ${QUERY} $2 2> /dev/null | \
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awk ' {n[$2]+=1;d[$2]+=$3} \
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END {for (i in n) \
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print i, n[i],d[i], d[i]/n[i]\
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}' | \
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sort -rnk4 | \
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egrep '^trn(I|M|fM)' | \
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tail -1 | \
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awk '{print $1,$NF}'
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rm -rf ${QUERY}
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}
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function gffTRNA {
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${ARAGORN} -w -io -seq $3 | awk -v gid=${1} -f ${WRAPARAGORN}
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}
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# s'alimente avec un fichier.fasta
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# $3 : nb de caractere du fichier, t : nb de caractere du titre,
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# $1+1 : nb de retour chariot du fichier
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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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# recupere les informations issues du programme repseek avec l'origine des deux
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# IR et leur taille
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function lookforIR {
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${REPSEEK} -c -p 0.001 $1 | \
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grep 'Distant.inv' | \
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sort -n -k4 | \
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tail -1 | \
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awk '{print $7}' | \
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sed 's/-/ /g'
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}
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# recupere le nom de la sequence analyse
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function seqName {
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head -n1 $1| \
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awk '{print $1}' | \
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sed 's/^>//' | \
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sed -E 's/.*\|([^|]+)\|/\1/'
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}
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# cree un resume du fichier analyse au format gff
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# ex : GFF (NC_*** Repseek IR1 start end . + . )
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function gffIR {
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lseq=$2
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nom=$1
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lookforIR $3 | \
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awk -v nom="$nom" -v lseq="$lseq" \
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'BEGIN {OFS="\t"} \
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{ startIR1=$1; \
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startIR2=$2; \
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endIR1=startIR1 + $3 -1; \
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endIR2=startIR2 + $3 -1; \
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startSSC=1; \
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endSSC=startIR1-1; \
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startLSC=endIR1+1; \
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endLSC=startIR2-1; \
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\
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print nom,"RepSeek","misc_feature",startSSC,endSSC,"\.","+","\.","ID=SSC;note=small single copy region";\
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print nom,"RepSeek","repeat_region",startIR1,endIR1,"\.","+","\.","ID=IRA;note=inverted repeat A";\
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print nom,"RepSeek","misc_feature",startLSC,endLSC,"\.","+","\.","ID=LSC;note=large single copy region";\
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print nom,"RepSeek","repeat_region",startIR2,endIR2,"\.","-","\.","ID=IRB;note=inverted repeat B";\
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}'
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}
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echo "##gff-version 3"
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genome=$1
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genome_name=`seqName $1`
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genome_length=`seqlength $1`
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gffIR ${genome_name} ${genome_length} ${genome}| grep -v '^ *$'
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gffTRNA ${genome_name} ${genome_length} ${genome}| grep -v '^ *$'
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@ -61,4 +61,4 @@ pushTmpDir ORG.ir
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popTmpDir
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exit 0
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exit 0
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@ -27,12 +27,14 @@
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
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ORG_DEBUG=1
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pushTmpDir ORG.normalize
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tmpfasta1="tmp_$$_1.fasta"
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tmpfasta2="tmp_$$_2.fasta"
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logdebug "Running on : $QUERY"
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loginfo "Computing the genome size..."
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genome_length=$(seqlength $QUERY)
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@ -47,7 +47,9 @@ function lookForIR {
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}
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SCDB="${IR_DATA_DIR}/SC_RefDB"
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QUERY="${CALL_DIR}/$1"
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openLogFile "${QUERY/.*/}.log"
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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@ -31,7 +31,7 @@ pushTmpDir ORG.buildSCDB
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loginfo "Building LSC coorientation graph..."
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${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${LOGFILE} > LSC.tgf
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${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${ORG_LOGFILE} > LSC.tgf
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${PROG_DIR}/cc.py LSC.tgf > LSC.cc
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loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
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loginfo "Done"
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@ -73,7 +73,7 @@ pushTmpDir ORG.buildSCDB
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loginfo "Checking LCS homogeneity..."
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${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${LOGFILE} > LSC_RefDB.tgf
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${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${ORG_LOGFILE} > LSC_RefDB.tgf
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${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
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NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
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if (( $NCC == 1 )); then
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@ -103,7 +103,7 @@ pushTmpDir ORG.buildSCDB
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loginfo "Building SSC coorientation graph..."
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${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${LOGFILE} > SSC.tgf
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${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${ORG_LOGFILE} > SSC.tgf
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${PROG_DIR}/cc.py SSC.tgf > SSC.cc
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loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
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loginfo "Done"
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@ -146,7 +146,7 @@ pushTmpDir ORG.buildSCDB
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loginfo "Checking SSC homogeneity..."
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${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${LOGFILE} > SSC_RefDB.tgf
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${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${ORG_LOGFILE} > SSC_RefDB.tgf
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${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
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NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
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if (( $NCC == 1 )); then
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42
detectors/trna/bin/go_trna.sh
Executable file
42
detectors/trna/bin/go_trna.sh
Executable file
@ -0,0 +1,42 @@
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#!/bin/bash
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#
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# Annotate tRNA
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#
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#========================================================================================
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#
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# Annotate tRNA based on the Aragorn software predictions.
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# go_trna.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.trna
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CAUTRNADB="${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
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export CAUTRNADB
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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TRNA=$(basename ${QUERY})
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aragorn -i -w -seq ${QUERY} | \
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${PROG_DIR}/../lib/aragorn_wrapper.awk
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popTmpDir
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exit 0
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@ -7,17 +7,9 @@ function genomeid() {
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return gid;
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}
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function home() {
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"echo $ORGANNOT_HOME" | getline homedir;
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return homedir;
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}
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function prog(program) {
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return home() "/" program;
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}
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function trnalib(prognam) {
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return home() "/lib/trnaCAU.ref.fasta";
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function trnalib() {
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"echo $CAUTRNADB" | getline ref;
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return ref
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}
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function awkPID() {
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@ -65,19 +57,20 @@ function patchtRNA(anticodon,trna,seq) {
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if (anticodon == "cat") {
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file=printfasta(trna "_" anticodon,seq,"");
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command= prog("sumatra") " -d -n " file " " trnalib();
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command= "sumatra -t 0.9 -x -n " file " " trnalib() " 2>> /dev/null";
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while ((command | getline output) > 0) {
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split(output,field," ");
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n[field[2]]++;
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d[field[2]]=field[3];
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match(field[2],"trn.M?");
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trna=substr(field[2],RSTART,RLENGTH);
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n[trna]+=field[5];
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}
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close(command)
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dmin=1;
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nmax=0;
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for (i in n) {
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dist=d[i]/n[i];
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if (dist < dmin) {
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dmin=dist;
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dist=n[i];
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if (n[i] > nmax) {
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nmax=n[i];
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trna=i;
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}
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}
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@ -94,6 +87,42 @@ function gene2product(gene) {
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return "tRNA-" AA3[substr(gene,4,1)];
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}
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function emblTRNA(geneid,trna,loc,anti,intron,seq) {
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if (loc ~ /^c/) {
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sub("c\\[","complement(",loc);
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sub("\\]",")",loc);
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sub(",","..",loc)}
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else {
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sub("\\[","",loc);
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sub("\\]","",loc);
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sub(",","..",loc)}
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anti=toupper(anti);
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gsub("T","U",anti);
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product=gene2product(trna);
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if (intron!="") {
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l=length(intron);
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intron=substr(intron,2,l-2);
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split(intron,intronpos,",");
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ib=intronpos[0];
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ie=intronpos[1];
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match(loc,"[0-9][0-9]*");
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gb=substr(loc,RSTART,RLENGTH);
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sub("\\.\\.",".." (gb + ib -2) "," (gb + ie) "..",loc); \
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sub("complement","complement(join",loc);\
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if (substr(loc,1,1) ~ /[0-9]/) {
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loc="join("loc}
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loc=loc")";
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}
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print "FT tRNA " loc;
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print "FT /gene=\""trna"\"";
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print "FT /anticodon=\""anti"\"";
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print "FT /product=\""product"("anti")\"";
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}
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function gffTRNA(geneid,trna,loc,anti,intron,seq) {
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if (loc ~ /^c/) {
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complement="-";
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@ -139,7 +168,6 @@ function gffTRNA(geneid,trna,loc,anti,intron,seq) {
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}
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BEGIN {
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print ARGV[1];
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AA1["Ala"]="A";
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AA1["Cys"]="C";
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AA1["Asp"]="D";
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@ -201,7 +229,7 @@ BEGIN {
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{ seq=epissage(intron,seq);
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trna=patchtRNA(anti,trna,seq);
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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gffTRNA(geneid,trna,loc,anti,intron,seq);
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emblTRNA(geneid,trna,loc,anti,intron,seq);
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seq=""
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}
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@ -225,5 +253,5 @@ BEGIN {
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END { seq=epissage(intron,seq);
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trna=patchtRNA(anti,trna,seq);
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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gffTRNA(geneid,trna,loc,anti,intron,seq);
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emblTRNA(geneid,trna,loc,anti,intron,seq);
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}
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47
organnote.sh
Executable file
47
organnote.sh
Executable file
@ -0,0 +1,47 @@
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#!/bin/bash
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#
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#
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#
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# Annotate tRNA
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#
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#========================================================================================
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#
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# Annotate tRNA based on the Aragorn software predictions.
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# go_trna.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/scripts/bash_init.sh"
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pushTmpDir ORG.organnot
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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RESULTS=$(basename ${QUERY/.*/})
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LOG="${CALL_DIR}/${RESULTS}.log"
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rm -f ${LOG}
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openLogFile ${LOG}
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
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${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
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${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
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cat "${RESULTS}.annot"
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popTmpDir
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@ -19,11 +19,18 @@ function getAbsolutePath {
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function pushTmpDir {
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TMP_DIR=$(mktemp -d -t "$1_proc_$$_")
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pushd $TMP_DIR >& /dev/null
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TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
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logdebug "Pushing temp directory $TMP_DIR"
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logdebug "Stack : ${TMP_DIR_STACK}"
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}
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function popTmpDir {
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TMP_DIR=$(echo $TMP_DIR_STACK | awk '{print $1}')
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TMP_DIR_STACK=$(echo $TMP_DIR_STACK | awk '{$1="";print $0}')
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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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@ -34,32 +41,42 @@ function errcho {
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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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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 ] $$ -- $1"
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if [[ ! -z ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA INFO ] $$ -- $1" >> ${LOGFILE}
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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 ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $1" >> ${LOGFILE}
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if [[ ! -z ${ORG_LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA ERROR ] $$ -- $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] $$ -- $1"
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if [[ ! -z ${LOGFILE} ]]; then
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echo `date +'%Y-%m-%d %H:%M:%S'` "[OA WARNING] $$ -- $1" >> ${LOGFILE}
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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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# Sequence related functions
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# Counts how many sequences are stored in a fasta file
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Reference in New Issue
Block a user