Mercurial > repos > bitlab > gecko
view gecko/bin/frags2align.sh @ 9:aec70bb1ae27 draft
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author | bitlab |
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date | Wed, 18 Nov 2020 08:08:25 +0000 |
parents | acbe7e0ef559 |
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#!/bin/bash if [ $# != 4 ]; then echo " ==== ERROR ... you called this script inappropriately." echo "" echo " usage: $0 fragsFILE.frags/.csv fastaX fastaY alignments.txt" echo "" exit -1 fi FRAGS=$1 FASTAX=$2 FASTAY=$3 ALIGN=$4 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" # generate indices $BINDIR/indexmaker $FASTAX $FASTAX.idx $BINDIR/indexmaker $FASTAY $FASTAY.idx $BINDIR/reverseComplement $FASTAY $FASTAY.rev $BINDIR/indexmaker $FASTAY.rev $FASTAY.rev.idx # extract frags if [ ${FRAGS: -4} == ".csv" ] then echo "....using csv" sed 's/,/ /g' $FRAGS > $FRAGS.fix $BINDIR/csvFrags2text $FRAGS.fix $FASTAX $FASTAY $FASTAY.rev $FASTAX.idx $FASTAY.idx $FASTAY.rev.idx $ALIGN rm $FRAGS.fix else echo "....using frags" $BINDIR/frags2text $FRAGS $FASTAX $FASTAY $FASTAY.rev $FASTAX.idx $FASTAY.idx $FASTAY.rev.idx $ALIGN fi rm $FASTAX.idx rm $FASTAY.idx rm $FASTAY.rev rm $FASTAY.rev.idx