master_blaster.sh

#!/bin/bash
#SBATCH --job-name=split_blast
#SBATCH --time=1:00:00
#SBATCH --chdir=.

module load python
module load anaconda
module load blast+/2.7.1


# Constants used by parts of the script
BLASTSCRIPT=split_blast.py
SPLIT_SCRIPT=split_fastas.py
DEFAULT_TEMP=temp
KEEPOUT=0
combine_file="combine_outputs.sh"
working_dir="$PWD"
time="5:00"
mem="1G"

sub_args=()
POSITIONAL=()
args=()

# make sure MASTER_BLASTER_PATH is defined
# or non-empty
if [[ -z "$MASTER_BLASTER_PATH" ]]; then
    echo MASTER_BLASTER_PATH must be defined, please refer to
    echo the 'install.sh' script.

    exit 1
fi    

# Run through all of the arguments provided from command line
while [[ $# -gt 0 ]]
do
key="$1"
if ! [[ -z "$key" ]]; then
    args+=("$1")
    args+=("$2")
fi

case $key in
    -q|--query)
    QUERY="$2"
    shift # past argument
    shift # past value
    ;;

    --ns|--nucSubject)
    NUCSUBJECT="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift # past argument
    shift # past value
    ;;

    --ps|--protSubject)
    PROTSUBJECT="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift # past argument
    shift # past value
    ;;

    --withColor)
    WITHCOLOR="$2"
    shift # past value
    ;;
-n|--numProcs)
    NUMPROCS="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    -t|--temp)
    TEMP="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    -b|--blastType)
    BLASTTYPE="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    --dontIndex)
    DONTINDEX="$1"          
    sub_args+=("$1")
    shift
    ;;


    -k|--keepOut)
    KEEPOUT=1
    sub_args+=("$1")
    shift
    shift
    ;;
    
    --blastFull)
    BLASTFULL="$2"
    sub_args+=("$1")
    shift
    ;;

    --task)
    TASK="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    --evalue)
    EVALUE="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;
    
    --outFmt)
    OUTFMT="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;
    
    --numHits)
    NUMHITS="$2"        
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    --numHsps)
    NUMHSPS="$2"          
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    --goodHit)
    GOODHIT="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;
    
    --orfSize)
    ORFSIZE="$2"
    sub_args+=("$1")
    sub_args+=("$2")
    shift
    shift
    ;;

    -h|--help)
    python $BLASTSCRIPT -h 
    echo '--time the amount of time to give jobs submitted to slurm.'
    echo '--mem the amount of memory to allocate for jobs submitted to slurm.'
    shift
    shift
    exit 1
    ;;

    --time)
    time="$2"
    shift
    shift
    ;;

    --mem)
    mem="$2"
    shift
    shift
    ;;

    *)
    POSITIONAL+=("$1")
    shift
    ;;
        
    
esac
done

if [ "$OUTFMT" = "" ]; then
    OUTFMT=5
fi
if [ -z "$TEMP" ]; then
    TEMP=$DEFAULT_TEMP
fi

# Read all of the command-line arguments into a variable
# Split the query file into multiple temporary files for blasting
if [ "$QUERY" ]; then
    srun $SPLIT_SCRIPT -q $(pwd)/$QUERY -t "$workign_dir$TEMP" --numProcs $NUMPROCS
else
    srun echo "Fasta query file must be provided for script to execute."
    exit 1
fi

# Get the number of files created by split_fastas
num_files= ls "$working_dir/$TEMP" | wc -l
output=0
# Call split_blast on the rest of the files in the directory 
# with the args passed in 
jobnumber=()
sub_args=($(echo "${sub_args[@]}" |tr ' ' '\n' | uniq | tr '\n' ' '))
shopt -s nullglob
for file in "$TEMP"/*
do
    # Create a file to run the blast, save its jobnumber 
    echo '#!/bin/sh' >> "$file.sh"
    echo '#SBATCH --time='$time >> "$file.sh"
    echo '#SBATCH --mem='$mem >> "$file.sh"
    echo '#SBATCH --output=pyoutput' >> $file.sh

    # We don't want to recreate the database for each blast, so only do it on the first
    if [[ -z "$jobnumber" ]] ; then
        echo ${sub_args[@]}
        echo module load python >> "$file.sh"
        echo module load anaconda >> "$file.sh"
        echo module load blast+/2.7.1 >> "$file.sh"

        echo python $MASTER_BLASTER_PATH/$BLASTSCRIPT -q $file ${sub_args[@]} >> "$file.sh"
    else
        # only depend on the first job, the one that created the db
        echo "#SBATCH --dependency=afterok"${jobnumber[0]} >> "$file.sh"
        echo module load python >> "$file.sh"
        echo module load anaconda >> "$file.sh"
        echo module load blast+/2.7.1 >> "$file.sh"

        echo python $MASTER_BLASTER_PATH/$BLASTSCRIPT -q $file ${sub_args[@]} --dontIndex >> "$file.sh"
    fi

    output=$( sbatch "$file.sh" )
    echo $output
    jobnumber+=(:"$( echo $output | cut -d ' ' -f 4 )")
done


# Combine files after the last blast has been completed
query_no_path=$(echo "$QUERY" | rev | cut -d '/' -f 1 | rev | cut -d '.' -f 1 )
echo "$query_no_path"
all_jobs=$(echo "${jobnumber[@]}" | tr -d '[:space:]')
sbatch --dependency=afterok$all_jobs $MASTER_BLASTER_PATH/$combine_file -t $TEMP $KEEPOUT "$query_no_path"