Mercurial > repos > alvarofaure > bitlab
comparison chromeister/bin/run_and_plot_chromeister.sh @ 0:7fdf47a0bae8 draft
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| author | alvarofaure |
|---|---|
| date | Wed, 12 Dec 2018 07:18:40 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:7fdf47a0bae8 |
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| 1 #!/usr/bin/env bash | |
| 2 G1=$1 | |
| 3 G2=$2 | |
| 4 KMER=$3 | |
| 5 DIM=$4 | |
| 6 | |
| 7 | |
| 8 FILE1=$(basename $G1) | |
| 9 FILE2=$(basename $G2) | |
| 10 | |
| 11 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" | |
| 12 | |
| 13 | |
| 14 if [ $# -lt 4 ]; then | |
| 15 echo "***ERROR*** Use: $0 <G1> <G2> <KMER> <DIMENSION>" | |
| 16 exit -1 | |
| 17 fi | |
| 18 | |
| 19 | |
| 20 | |
| 21 (time $BINDIR/CHROMEISTER -query $G1 -db $G2 -kmer $KMER -out $FILE1-$FILE2.mat -dimension $DIM) &> $FILE1-$FILE2.log | |
| 22 (Rscript $BINDIR/compute_score.R $FILE1-$FILE2.mat $DIM) &> $FILE1-$FILE2.scr.txt | |
| 23 | |
| 24 #$BINDIR/plot.R $FILE1-$FILE2.mat | |
| 25 | |
| 26 | |
| 27 #rm $FILE1-$FILE2.mat |