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view gecko/bin/comparison.sh @ 1:35af401890c0 draft
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author | bitlab |
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date | Thu, 13 Dec 2018 07:59:25 -0500 |
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#!/bin/bash FL=1000 # frequency limit if [ $# != 7 ]; then echo " ==== ERROR ... you called this script inappropriately." echo "" echo " usage: $0 seqXName seqYName lenght similarity WL fixedL strand" echo "" exit -1 fi seqXName=$(basename "$1") extensionX="${seqXName##*.}" seqXName="${seqXName%.*}" seqYName=$(basename "$2") extensionY="${seqYName##*.}" seqYName="${seqYName%.*}" #seqXName=`basename $1 .fasta` #seqYName=`basename $2 .fasta` BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" length=${3} similarity=${4} WL=${5} # wordSize fixedL=${6} strand=${7} distance=$((4*${WL})) if [[ ! -f ../hits/${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ]]; then echo "${BINDIR}/hits ${seqXName} ${seqYName} ${seqXName}-${seqYName}-K${WL}.hits ${FL} ${WL}" ${BINDIR}/hits ${seqXName} ${seqYName} ${seqXName}-${seqYName}-K${WL}.hits ${FL} ${WL} echo "${BINDIR}/sortHits 10000000 32 ${seqXName}-${seqYName}-K${WL}.hits ${seqXName}-${seqYName}-K${WL}.hits.sorted" ${BINDIR}/sortHits 10000000 32 ${seqXName}-${seqYName}-K${WL}.hits ${seqXName}-${seqYName}-K${WL}.hits.sorted echo "${BINDIR}/filterHits ${seqXName}-${seqYName}-K${WL}.hits.sorted ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${WL}" ${BINDIR}/filterHits ${seqXName}-${seqYName}-K${WL}.hits.sorted ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${WL} mv ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ../hits/ fi ln -s ../hits/${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered . echo "${BINDIR}/FragHits $1 $2 ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${seqXName}-${seqYName}-s${strand}.frags ${length} ${similarity} ${WL} ${fixedL} ${strand}" ${BINDIR}/FragHits $1 $2 ${seqXName}-${seqYName}-K${WL}.hits.sorted.filtered ${seqXName}-${seqYName}-s${strand}.frags ${length} ${similarity} ${WL} ${fixedL} ${strand} echo "--------------------DONE------------------"