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1
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1 #!/bin/bash
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2
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3 FL=1000 # frequency limit
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4
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5 if [ $# != 7 ]; then
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6 echo " ==== ERROR ... you called this script inappropriately."
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7 echo ""
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8 echo " usage: $0 seqXName seqYName lenght similarity WL fixedL strand"
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9 echo ""
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10 exit -1
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11 fi
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12
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13 seqXName=$(basename "$1")
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14 extensionX="${seqXName##*.}"
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15 seqXName="${seqXName%.*}"
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16
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17 seqYName=$(basename "$2")
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18 extensionY="${seqYName##*.}"
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19 seqYName="${seqYName%.*}"
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20
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21 #seqXName=`basename $1 .fasta`
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22 #seqYName=`basename $2 .fasta`
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23
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24 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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25
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26 length=${3}
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27 similarity=${4}
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28 WL=${5} # wordSize
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29 fixedL=${6}
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30 strand=${7}
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31 distance=$((4*${WL}))
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32
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33 if [[ ! -f ../hits/${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ]]; then
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34 echo "${BINDIR}/hits ${seqXName} ${seqYName} ${seqXName}-${seqYName}-K${WL}.hits ${FL} ${WL}"
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35 ${BINDIR}/hits ${seqXName} ${seqYName} ${seqXName}-${seqYName}-K${WL}.hits ${FL} ${WL}
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36
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37 echo "${BINDIR}/sortHits 10000000 32 ${seqXName}-${seqYName}-K${WL}.hits ${seqXName}-${seqYName}-K${WL}.hits.sorted"
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38 ${BINDIR}/sortHits 10000000 32 ${seqXName}-${seqYName}-K${WL}.hits ${seqXName}-${seqYName}-K${WL}.hits.sorted
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39
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40 echo "${BINDIR}/filterHits ${seqXName}-${seqYName}-K${WL}.hits.sorted ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${WL}"
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41 ${BINDIR}/filterHits ${seqXName}-${seqYName}-K${WL}.hits.sorted ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${WL}
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42
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43 mv ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ../hits/
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44 fi
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45
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46 ln -s ../hits/${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered .
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47
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48 echo "${BINDIR}/FragHits $1 $2 ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${seqXName}-${seqYName}-s${strand}.frags ${length} ${similarity} ${WL} ${fixedL} ${strand}"
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49 ${BINDIR}/FragHits $1 $2 ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${seqXName}-${seqYName}-s${strand}.frags ${length} ${similarity} ${WL} ${fixedL} ${strand}
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50
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51 echo "--------------------DONE------------------"
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52
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