run_mlst

#!/bin/bash

# Help function
show_help() {
    echo "Usage: $0 <runid> <sampleid> [--blastdb path] [--datadir path]"
    echo
    echo "Required arguments:"
    echo "  runid        Run ID (format: XYYYY...)"
    echo "  sampleid     Sample ID"
    echo
    echo "Optional arguments:"
    echo "  --blastdb    Path to BLAST database (default: /home/mdu/resources/mlst/blast/mlst.fa)"
    echo "  --datadir    Path to MLST data directory (default: /home/mdu/resources/mlst/pubmlst)"
    echo
    echo "Before running the script:"
    echo "  conda activate /home/khhor/conda/envs/mlst/"
}

# Default values
BLASTDB="/home/mdu/resources/mlst/blast/mlst.fa"
DATADIR="/home/mdu/resources/mlst/pubmlst"

# Parse arguments
if [ "$#" -lt 2 ]; then
    show_help
    exit 1
fi

runid=$1
sampleid=$2
shift 2

# Parse optional arguments
while [ "$#" -gt 0 ]; do
    case "$1" in
        --blastdb) BLASTDB="$2"; shift 2;;
        --datadir) DATADIR="$2"; shift 2;;
        --help|-h) show_help; exit 0;;
        *) echo "Unknown parameter: $1"; show_help; exit 1;;
    esac
done

# Extract YYYY from runid
YYYY=${runid:1:4}

# Change directory
# cd "/home/mdu/qc/$YYYY/$runid" || { echo "Directory not found"; exit 1; }

echo "Output for spades:"
mlst --quiet --blastdb "$BLASTDB" --datadir "$DATADIR" --nopath /home/mdu/data/"$runid"/"$sampleid"/spades/spades.fa --exclude ecoli

echo "Output for shovill:"
mlst --quiet --blastdb "$BLASTDB" --datadir "$DATADIR" --nopath /home/mdu/data/"$runid"/"$sampleid"/shovill/current/contigs.fa --exclude ecoli

echo "Output for skesa:"
mlst --quiet --blastdb "$BLASTDB" --datadir "$DATADIR" --nopath /home/mdu/data/"$runid"/"$sampleid"/skesa/current/skesa.fa --exclude ecoli