All-hhblits.sh
From Bioinformatikpedia
This bash script was used to perform HHBlits search in task 2.
Source
<source lang="bash">
- !/bin/sh -e
PRKT=$HOME/master-practical-2013 TASK1=$PRKT/task01 TASK2=$PRKT/task02/01-seq-search EXE=/usr/bin/hhblits OUT=$TASK2/results DATA=$PRKT/data DB=$DATA/hhblits/uniprot20_current
for query in $TASK1/*.fasta do filename=`basename ${query}` echo "hhblits processing query '$filename' ..." echo "$EXE -d $DB -i ${query} \ -o $OUT/hhblits_$filename.hhr \ -oa3m $OUT/hhblits_$filename.a3m \ -ohhm $OUT/hhblits_$filename.hhm \ -oalis $OUT/hhblits_$filename.alis \ -Z 200000 -B 200000" | batch echo "hhblits for query sequence '$filename' is done!" done </source>
