All-psiblast.sh
This bash script was used for all PSI-Blast search in task 2.
Source
<source lang="bash">
- !/bin/sh
PRKT=$HOME/master-practical-2013 TASK1=$PRKT/task01 TASK2=$PRKT/task02/01-seq-search EXE=/usr/bin/blastpgp OUT=$TASK2/results DATA=$PRKT/data DB=$DATA/big/big_80
for query in $TASK1/*.fasta; do filename=`basename $query` for iter in 2 10 do for e in 0.002 '10e-10' do echo "Iteration $iter, E-val $e is running ..." #output in tsv format echo "$EXE -d $DB -i ${query} -m 9 -j $iter -h $e \ -b 200000 \ > $OUT/psiblast-${iter}_iterations_eval_$e-${filename}.tsv" \ | batch #output in xml format #$EXE -d $DB -i ${query} -j $iter -h $e \ # -m 7 -b 200000 \ # -C $OUT/psiblast-${iter}_iterations_eval_$e-${filename}.chk \ # > $OUT/psiblast-${iter}_iterations_eval_$e-${filename}.xml #echo "Iteration $iter, E-val $e is done for $filename" done done done </source>
