First version of if inverted repeat annotation tools
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detectors/ir/.DS_Store
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detectors/ir/.DS_Store
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detectors/ir/bin/go_ir.sh
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detectors/ir/bin/go_ir.sh
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@ -0,0 +1,64 @@
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#!/bin/bash
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#
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# Annotate the Inverted Repeats of a plastide genome
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#
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#========================================================================================
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#
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# The SSC and LSC are approximatively mapped by similarity with a reference database
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# Inverted repeats (IRs) are identified for maximizing the segregation between
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# LSC and SSC match
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#
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#
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# go_normalize.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to normalize
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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 ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh
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pushTmpDir ORG.ir
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loginfo "Computing the genome size..."
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genome_length=$(seqlength $QUERY)
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loginfo " --> $genome_length bp"
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loginfo "Done"
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IR=( $(lookForIR ${QUERY}) )
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posIR1=${IR[4]}
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posIR2=${IR[6]}
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let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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beginLSC=1
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let "endLSC=$posIR1-1"
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let "beginSSC=$endIR1+1"
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let "endSSC=$posIR2-1"
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echo "FT misc_feature ${beginLSC}..${endLSC}"
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echo "FT /note=\"large single copy region (LSC)\""
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echo "FT repeat_region ${posIR1}..${endIR1}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat B; IRB\""
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echo "FT misc_feature ${beginSSC}..${endSSC}"
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echo "FT /note=\"small single copy region (SSC)\""
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echo "FT repeat_region ${posIR2}..${endIR2}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat A; IRA\""
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popTmpDir
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exit 0
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@ -3,104 +3,37 @@
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# NORMALISATION D'UN PLASTIDE
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#
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#========================================================================================
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# Ce programme dispose de 4 fonctions pour traiter les donnees fasta issues de genbank
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# - seqlength : compte le nombre de paire de base du fichier
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# ex : seqlength $1
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#
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# - cutseq : permet de couper un morceau de la sequence
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# cutseq [x] [y]
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# [x] : coordonne du debut de la sequence a couper
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# [y] : coordonne de la fin de la sequence a couper
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# ex : cutseq $1 10 100
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# Normalize the way the chloroplaste genome sequence is linearized in the fasta file
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# The normalized sequence is:
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#
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# LSC + IRB + SSC + IRA
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#
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# - revcomp : donne le brin reverse
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# ex : $1 | revcomp
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# The SSC and LSC are approximatively mapped by similarity with a reference database
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# Inverted repeats (IRs) are identified for maximizing the segregation between
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# LSC and SSC match
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#
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#
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# - formatfasta : permet de coller a la suite plusieurs morceaux de sequence au moment de
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# la reecriture
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# - joinfasta : enleve les titres au moment de la reecriture du fichier et renvoie les
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# informations dans la fonction formatfasta
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# ex : joinfasta $1
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# go_normalize.sh <FASTAFILE>
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#
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#========================================================================================
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# Pour lancer le programme, utiliser les commandes :
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# chmod +x normalize_plastid.sh
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#./normalize_plastid.sh [fichier].fasta
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# - <FASTAFILE> : The fasta file containing the genome to normalize
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#
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# ex : seqlength $1
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# Results are printed to the standart output
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#
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# cutseq $1 [x] [y]
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# [x]:coordonne du debut [y]:coordonne de la fin de la sequence a couper
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# ex : cutseq $1 10 100
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#
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# ex : $1 | revcomp
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#
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# ex : joinfasta $1
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
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function lookForIR {
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local QUERY="$1"
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local MATCHES=$(basename ${QUERY})
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MATCHES="${MATCHES/.*/.matches}"
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local REPEATS="${MATCHES/.*/.repseek}"
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loginfo "Locating SSC and LSC by similarity..."
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blastn -db ${SCDB} \
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-query ${QUERY} \
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-outfmt 6 \
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-max_target_seqs 10000 | \
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awk '($4 > 1000) && ($3>80) { \
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SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
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if ($7 < $8) \
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{print substr($2,1,3),$7,$8,SAME} \
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else \
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{print substr($2,1,3),$8,$7,SAME}}' | \
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sort -nk 2 > ${MATCHES}
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loginfo "Done"
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loginfo "Looking for long inverted repeats..."
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repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
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loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
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loginfo "Done"
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loginfo "Marking and selecting the best inverted repeat..."
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local IR=( $(${PROG_DIR}/selectIR.py ${MATCHES} ${REPEATS}) )
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loginfo "Done"
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loginfo " --> IR size : IRa = ${IR[5]} / IRb = ${IR[7]}"
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loginfo " --> IR Score: ${IR[8]}"
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let "deltaIR=${IR[5]} - ${IR[7]}"
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if (( $deltaIR < -10 )) || (( $deltaIR > 10 )); then
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logwarning "Differences between IR lengths ($deltaIR) is greater than 10"
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fi
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echo "${IR[@]}"
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}
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pushTmpDir ORG.normalize
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SCDB="${IR_DATA_DIR}/SC_RefDB"
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QUERY="${CALL_DIR}/$1"
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MATCHES="${1/.*/.matches}"
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REPEATS="${1/.*/.repseek}"
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tmpfasta1="tmp_$$_1.fasta"
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tmpfasta2="tmp_$$_2.fasta"
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openLogFile "${QUERY/.*/.log}"
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loginfo "Computing the genome size..."
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genome_length=$(seqlength $QUERY)
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loginfo " --> $genome_length bp"
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@ -136,7 +69,7 @@ pushTmpDir ORG.normalize
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rm -f ${tmpfasta1}
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QUERY=${tmpfasta2}
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loginfo "Recompute location of the IR..."
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loginfo "Recomputing location of the IR..."
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declare -a IR=( $(lookForIR ${QUERY}) )
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loginfo "Done"
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@ -224,7 +157,7 @@ pushTmpDir ORG.normalize
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fi
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# Merges the four parts of the genome.
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cat ${tmpSSC} ${tmpIR1} ${tmpLSC} ${tmpIR2} | joinfasta
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cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
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53
detectors/normalize/lib/lookforIR.lib.sh
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53
detectors/normalize/lib/lookforIR.lib.sh
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
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function lookForIR {
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local QUERY="$1"
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local MATCHES=$(basename ${QUERY})
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MATCHES="${MATCHES/.*/}.matches"
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local REPEATS="${MATCHES/.*/}.repseek"
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loginfo "Locating SSC and LSC by similarity..."
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blastn -db ${SCDB} \
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-query ${QUERY} \
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-outfmt 6 \
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-max_target_seqs 10000 | \
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awk '($4 > 1000) && ($3>80) { \
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SAME=(($7 < $8) && ($9 < $10)) || (($7 > $8) && ($9 > $10)); \
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if ($7 < $8) \
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{print substr($2,1,3),$7,$8,SAME} \
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else \
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{print substr($2,1,3),$8,$7,SAME}}' | \
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sort -nk 2 > ${MATCHES}
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loginfo "Done"
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loginfo "Looking for long inverted repeats..."
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repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
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loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
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loginfo "Done"
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loginfo "Marking and selecting the best inverted repeat..."
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local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
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loginfo "Done"
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loginfo " --> IR size : IRa = ${IR[5]} / IRb = ${IR[7]}"
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loginfo " --> IR Score: ${IR[8]}"
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let "deltaIR=${IR[5]} - ${IR[7]}"
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if (( $deltaIR < -10 )) || (( $deltaIR > 10 )); then
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logwarning "Differences between IR lengths ($deltaIR) is greater than 10"
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fi
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echo "${IR[@]}"
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}
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SCDB="${IR_DATA_DIR}/SC_RefDB"
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QUERY="${CALL_DIR}/$1"
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openLogFile "${QUERY/.*/}.log"
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