3_analyze-plasmids

#!/bin/bash -ex

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 plasmids. 
        default is /n/scratch3/users/a/ak586/microtrawler/3_analysis-plasmid
    "    
}

merge_mlplasmid_output() {
    STRAIN="$1"
    STRAINNOSPACE=$(echo $1 | sed 's/ /_/g')
    echo -e "AccNum\tProb_Chrom\tProb_Plasmid\tPrediction\tContig_name\tContig_len" > "$OUTPUTDIR/merged-$STRAINNOSPACE-mlplasmidout"
    while read -r i; do
        acc=$(basename $(dirname $i))
        sed 1d $i/plasmid/mlplasmids_out.tab | sed "s:^:$acc\t:g" >> "$OUTPUTDIR/merged-$STRAINNOSPACE-mlplasmidout"
    done<"$INPUTDIR/output_$STRAINNOSPACE-dirs"
}

merge_plasmidfinder_output() {
    echo -e "AccNum\tDatabase\tPlasmidGroup\tIdentity\tQ/TLen\tContig\tPosition\tNote\tDBAcc" > $OUTPUTDIR/merged-plasmidfinder
    for i in $INPUTDIR/NCTC/ena/*/*/plasmid; do 
        acc=$(basename $(dirname $(dirname $i)))
        #cat $i/results_tab.tsv
        sed 1d $i/results_tab.tsv | awk -F'\t' 'BEGIN { OFS = "\t" } {print $1,$2,$3,$4,$5,$6,$7,$8}' | sed "s:^:$acc\t:g" >> "$OUTPUTDIR/merged-plasmidfinder"
    done
}

merge_mob_output() {
    rm -f $OUTPUTDIR/merged-contigreport 2> /dev/null
    rm -f $OUTPUTDIR/merged-mobtyper 2> /dev/null
    for i in $INPUTDIR/NCTC/ena/*/*/mob_out/contig_report.txt; do
        #echo $i
        accnum=$(basename $(dirname $(dirname $(dirname $i))))
        if [ ! -s $OUTPUTDIR/merged-contigreport ]; then
            head -1 $i | sed 's/^/AccNum\t/'> $OUTPUTDIR/merged-contigreport
        fi
        grep 'plasmid' $i | sed "s/^/$accnum\t/" >> $OUTPUTDIR/merged-contigreport
    done
    for i in $INPUTDIR/NCTC/ena/*/*/mob_out/mobtyper_results.txt; do
        accnum=$(basename $(dirname $(dirname $(dirname $i))))
        if [ ! -s $OUTPUTDIR/merged-mobtyper ]; then
            head -1 $i | sed 's/^/AccNum\t/' > $OUTPUTDIR/merged-mobtyper
        fi
        count=$(echo $(wc -l $i) |awk '{print $1}')
        if [ $count -eq 1 ]; then
            echo $i
            exit
        fi
        sed 1d $i | sed "s/^/$accnum\t/" >> $OUTPUTDIR/merged-mobtyper
    done

}

main() {
    INPUTDIR="/n/scratch3/users/a/ak586/microtrawler/2_analyze-seqs"
    OUTPUTDIR="/n/scratch3/users/a/ak586/microtrawler/3_analysis-plasmid"
    for i in "$@"; do
    case $i in
        -i|--inputdir)
        INPUTDIR="$2"
        shift
        shift
        ;;
        -o|--outputdir)
        OUTPUTDIR="$2"
        shift
        shift
        ;;
        -h|--help)
        usage
        exit
        ;;
        *)
        ;;
    esac
    done

    mkdir -p $OUTPUTDIR
    #merge_plasmidfinder_output
    merge_mob_output
    #for i in "Klebsiella pneumoniae" "Escherichia coli" "Enterococcus faecium" "Enterococcus faecalis" "Acinetobacter baumannii"
    #do
        #merge_mlplasmid_output "$i"
    #done
}
main "$@"