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#!/bin/bash
#SBATCH -c 8            # number of "cores"
#SBATCH -t 4:00:00     # time in d-hh:mm:ss
#SBATCH -p serial       # partition
#SBATCH -q normal       # QOS
#SBATCH -e slurm.%j%A_%a.err # file to save job's STDERR (%jfor = JobId)each sub-job
#SBATCH --export=NONE   # Purge the job-submitting shell environment
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=spock@asu.edu

# process the manifest file
manifest="${1:?ERROR -- must pass a manifest file}"
taskid=$SLURM_ARRAY_TASK_ID
case=$(getline $taskid $manifest | cut -f 1 -d ' ')
fasta=$(getline $taskid $manifest | cut -f 2 -d ' ')

# set up sbatch parameters and env
module purge
module load anaconda/py3
source activate bat

# set up input and output file names
base=$(basename -s .fasta $fasta)
out1=/scratch/name/"$base"_${case}_fmt11.txt
out2=/scratch/name/"$base"_${case}_fmt6.txt

# put all the blastx flags here just for the sake of formatting
args=(
 -query $fasta
 -db /scratch/name/path/db/$case/$case
 -evalue 1e-3
 -num_threads $(nproc)
 -max_target_seqs 5
 -max_hsps 1
 -outfmt '11'
 -out $out1
)
blastx "${args[@]}"

blast_formatter -archive $out1 -outfmt "6 qseqid sseqid evalue" -out $out2