anvi-script-prep-clinker.sh

#!/bin/bash

print_usage() {
    echo "anvi-script-prep-clinker [-a <annotation-source>] -i <in-dir> -o <out-dir>"
    echo ""
    echo "Description:"
    echo "  Takes a directory of exported locus databases (generated by"
    echo "  anvi-export-locus) and converts them to Genbank files to be"
    echo "  used with clinker. These GB files will be placed in the"
    echo "  provided output directory."
    echo ""
    echo "  The optional argument -a allows the user to specify which"
    echo "  annotation source from the input locus databases to be added"
    echo "  to the resulting GB files. However, this option is incompatible"
    echo "  with Anvi'o versions 7.1 and earlier, where only COG_FUNCTION"
    echo "  can be added to the output. Only use the -a option with Anvi'o"
    echo "  versions later than 7.1, such as the dev environment."
    echo ""
    echo "  Depends on the following scripts, which must be in the same"
    echo "  base directory as this script:"
    echo "   - gff_to_genbank.py"
    echo "   - - GFFParser.py"
    echo "   - clean-gff-products.sh"
}

indir=""
outdir=""
annotation=""

while getopts ":hi:o:a:" opt; do
    case $opt in
        h)  print_usage
            exit 1
            ;;
        i)  indir="${OPTARG}"
            ;;
        o)  outdir=$(realpath ${OPTARG})
            ;;
        a)  annotation="${OPTARG}"
            ;;
        \?) echo "Invalid option: -${OPTARG}. Use the -h option for more information.">&2
            exit 1
            ;;
        :)  echo "Option -$OPTARG requires an argument. Use the -h option for more information.">&2
            exit 1
            ;;
    esac
done

if [[ -z "$indir" ]]; then
    echo "You must provide an input directory."
    exit 1
fi

if [[ ! -d "$indir" ]]; then
    echo "The provided directory does not exist: $indir"
    exit 1
fi

if [[ ! $CONDA_DEFAULT_ENV =~ "anvio" ]]; then
    echo "You need to activate an anvio conda environment before running this."
    exit 1
fi

# Get real directory where script file is located,
# even if the script was called via a symlink
SOURCE=${BASH_SOURCE[0]}
while [ -L "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
  DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )
  SOURCE=$(readlink "$SOURCE")
  [[ $SOURCE != /* ]] && SOURCE=$DIR/$SOURCE # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR=$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )

# Extract GFF of annotations
for f in ${indir}/*.db; do
    if [[ -z "$annotation" ]]; then
        anvi-get-sequences-for-gene-calls -c $f --export-gff3 -o ${f%.db}.gff
    else
        anvi-get-sequences-for-gene-calls -c $f --export-gff3 -o ${f%.db}.gff --annotation-source "$annotation"
    fi
done

echo "Cleaning GFFs of reserved characters..."
# Clean the GFFs of reserved characters
for f in ${indir}/*.gff; do
    $DIR/clean-gff-products.sh $f
done

echo "Converting to GenBank format..."
# Convert GFF to GB format
for f in ${indir}/*.gff; do
    $DIR/gff_to_genbank.py $f ${f%.gff}.fa
done

# Copy GB files for clinker to the output directory
cp ${indir}/*.gb $outdir

echo "Done!"