#!/bin/bash

WORKDIR="/lustre/users/${USER}/blast_proj"
INPUT_FASTA=${WORKDIR}/data_set.fa.gz
BLAST_E_VAL="1e-3"
BLAST_DB="/mnt/lustre/bsp/NCBI/BLAST/nr"
THREADS=24
BLAST_HOURS=0
BLAST_MINUTES=30
ID_FMT="%01d"
SPLIT_PREFIX="sub_set"
MAIL_ADDRESS="youremail@somewhere.ac.za"

zcat ${INPUT_FASTA} | csplit -z -f ${WORKDIR}/${SPLIT_PREFIX} -b "${ID_FMT}.split.fasta" - '/^>/' '{*}'

NUM_PARTS=$(ls sub_set*.split.fasta | wc -l)
START=0
END=$(expr $NUM_PARTS - 1)

TMPSCRIPT=thejob.sh
# note: make a distinction between variables set by the containing script (e.g. WORKDIR) and
# ones set in the script (e.g. INDEX). The ones set in the script need to be escaped out
cat >${TMPSCRIPT} << END
#!/bin/bash
#PBS -l select=1:ncpus=${THREADS}
#PBS -l place=excl:group=nodetype
#PBS -l walltime=${BLAST_HOURS}:${BLAST_MINUTES}:00
#PBS -q normal
#PBS -m ae
#PBS -M ${MAIL_ADDRESS}

. /etc/profile.d/modules.sh
module add chpc/BIOMODULES
module add ncbi-blast/2.6.0

INDEX="${WORKDIR}/${SPLIT_PREFIX}\${PBS_ARRAY_INDEX}"
INFILE="\${INDEX}.split.fasta"
OUTFILE="\${INDEX}.blastx.xml"

cd ${WORKDIR}
blastx -num_threads 8 -evalue ${BLAST_E_VAL} -db ${BLAST_DB} -outfmt 5 -query \${INFILE} -out \${OUTFILE} END

BLAST_JOBID=$(qsub -N sunblast -J ${START}-${END} ${TMPSCRIPT} | cut -d. -f1)
echo "submitted: ${BLAST_JOBID}"

rm ${TMPSCRIPT}

cat >${TMPSCRIPT} << END
#!/bin/bash
#PBS -l select=1:ncpus=1
#PBS -l place=free
#PBS -l walltime=1:00:00
#PBS -q workq
#PBS -m ae
#PBS -M ${MAIL_ADDRESS}
#PBS -W depend=afterok:${BLAST_JOBID}

cd ${WORKDIR}
tar jcf blast-xml-output.tar.bz2 *.blastx.xml
END

qsub -N tarblast ${TMPSCRIPT}

rm ${TMPSCRIPT}