INNER CODE UNIT · Shell

taxids

pirovc/genome_updater · genome_updater.sh:1372

    taxids=${taxids// /} # remove spaces
elif [[ "${tax_mode}" =~ ^gtdb ]]; then
    IFS=","
    for tx in ${taxids}; do
        if [[ ! "${tx}" =~ ^[\\^]{1}?[dpcofgs]__.* ]]; then
            echo "${tx}: invalid taxid"
            exit 1
        fi
    done
    IFS=$' '
fi

# top assemblies by rank
if [[ ! "${top_assemblies}" =~ ^[0-9]+$ && ! "${top_assemblies}" =~ ^(domain|phylum|class|order|family|genus|species)\:[1-9][0-9]*$ ]]; then
    echo "${top_assemblies}: invalid top assemblies - should be a number > 0 or [domain|phylum|class|order|family|genus|species]:number"
    exit 1
else
    top_assemblies_rank=""

View source record →