3_analyze-crispr

#!/bin/bash -e

wd=$(pwd)
source ./paths
source ./funcs

usage() {
    echo "
    -i,--inputdir : input directory of output from step 2. 
            default is /n/scratch3/users/a/ak586/microtrawler/2_analyze-seqs
    -o,--outputdir: base output directory for rgi. 
        default is /n/scratch3/users/a/ak586/microtrawler/3_analysis-crispr
    -d,--dbdir: input directory of output from step 0. 
        default is /n/scratch3/users/a/ak586/microtrawler/0_databases
    -f,--fastadir: input directory of output from step 1. 
        default is /n/scratch3/users/a/ak586/microtrawler/1_sequences
    "    
}

merge_crispr_output() {

}

main() {
    INPUTDIR="/n/scratch3/users/a/ak586/microtrawler/2_analyze-seqs"
    OUTPUTDIR="/n/scratch3/users/a/ak586/microtrawler/3_analysis-crispr"
    DBDIR="/n/scratch3/users/a/ak586/microtrawler/0_databases"
    FASTADIR="/n/scratch3/users/a/ak586/microtrawler/1_sequences"
    for i in "$@"; do
    case $i in
        -i|--inputdir)
        INPUTDIR="$2"
        shift
        shift
        ;;
        -d|--dbdir)
        DBDIR="$2"
        shift
        shift
        ;;
        -f|--fastadir)
        FASTADIR="$2"
        shift
        shift
        ;;
        -o|--outputdir)
        OUTPUTDIR="$2"
        shift
        shift
        ;;
        -h|--help)
        usage
        exit
        ;;
        *)
        ;;
    esac
    done

    mkdir -p $OUTPUTDIR
    merge_crispr_output
}
main "$@"