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view chromeister/bin/allVsAll.sh @ 0:ee6b15b409e5 draft
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author | bitlab |
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date | Thu, 13 Dec 2018 06:27:57 -0500 |
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#!/usr/bin/env bash DIR=$1 EXT=$2 DIM=$3 KMER=$4 array=() x=0 if [ $# != 4 ]; then echo "***ERROR*** Use: $0 genomesDirectory extension dim kmer" exit -1 fi indexnameA=$(basename "$DIR") BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}') do array[$x]=$elem x=`expr $x + 1` #echo "X: $elem" done for ((i=0 ; i < ${#array[@]} ; i++)) do for ((j=i ; j < ${#array[@]} ; j++)) do if [ $i != $j ]; then seqX=${array[$i]} seqY=${array[$j]} echo "----------${seqX}-${seqY}-----------" if [[ ! -f ${seqX}.$EXT-${seqY}.$EXT.mat ]]; then $BINDIR/run_and_plot_chromeister.sh $DIR/${seqX}.$EXT $DIR/${seqY}.$EXT $KMER $DIM #Rscript $BINDIR/compute_score.R $seqX.$EXT-$seqY.$EXT.mat $DIM > $seqX.$EXT-$seqY.$EXT.scr.txt fi fi done done # generate index if [[ ! -f index.csv.temp ]] && [ ! -f index-$indexnameA.csv ]; then echo "Launching... $BINDIR/index_chromeister_solo.sh index-$indexnameA.csv $DIR $DIR" $BINDIR/index_chromeister_solo.sh . index-$indexnameA.csv $DIR $DIR fi