builddb.sh

#!/bin/bash

#
# Prepare database for CLARK, CLAssifier based on Reduced K-mers.
#
if [ $# -ne 4 ]; then
    echo "Usage: $0 <DB directory path> <taxondata dir> <DB name> <taxonomy rank>"
    exit
fi

#EXE=$(dirname "$0")
EXE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DBDR=$1
TAXDR=$2
DB=$3
RANK=$4

if [ -s "$TAXDR/nucl_gb.accession2taxid.7z" ]; then
        GB_STREAM="7z x -so"
        GB_EXT=".7z"
fi
if [ -s "$TAXDR/nucl_gb.accession2taxid.gz" ]; then
        GB_STREAM="gunzip -c"
        GB_EXT=".gz"
fi
if [ -s "$TAXDR/nucl_gb.accession2taxid" ]; then
        GB_STREAM="cat"
        GB_EXT=""
fi
if [ -s "$TAXDR/nucl_wgs.accession2taxid.7z" ]; then
        WGS_STREAM="7z x -so"
        WGS_EXT=".7z"
fi
if [ -s "$TAXDR/nucl_wgs.accession2taxid.gz" ]; then
        WGS_STREAM="gunzip -c"
        WGS_EXT=".gz"
fi
if [ -s "$TAXDR/nucl_wgs.accession2taxid" ]; then
        WGS_STREAM="cat"
        WGS_EXT=""
fi


if [ -s "$TAXDR/taxdump.tar.gz" ]; then
    echo "Uncompressing taxonomy data files... "
    pushd "$TAXDR"
    tar -zxf taxdump.tar.gz
    popd
fi

if [ ! -s "$TAXDR/nodes.dmp" ] || [ ! -s "$TAXDR/merged.dmp" ]; then
    echo "No taxonomy data found in $TAXDR, aborting"
    exit 1
fi

if [ ! -f "$DBDR/.$DB" ]; then
    echo "Failed to find list of library files: $DBDR/.$DB, aborting"
        exit 2
fi
rm -f "$DBDR/.tmp" "$DBDR/targets.txt" "$DBDR/.settings" "$DBDR/files_excluded.txt"

if [ ! -s "$DBDR/.$DB.fileToAccssnTaxID" ] ; then
    echo "Re-building $DB.fileToAccssnTaxID"
    ($GB_STREAM "$TAXDR/nucl_gb.accession2taxid$GB_EXT"; $WGS_STREAM "$TAXDR/nucl_wgs.accession2taxid$WGS_EXT") | "$EXE/getAccssnTaxID" "$DBDR/.$DB" "$TAXDR/merged.dmp" > "$DBDR/.$DB.fileToAccssnTaxID"
fi
if [ ! -s "$DBDR/.$DB.fileToTaxIDs" ]; then
    echo "Retrieving taxonomy nodes for each sequence based on taxon ID..."
    "$EXE/getfilesToTaxNodes" "$TAXDR/nodes.dmp" "$DBDR/.$DB.fileToAccssnTaxID" > "$DBDR/.$DB.fileToTaxIDs"
fi
if [ -s "$DBDR/.$DB.fileToTaxIDs" ]; then
    pushd "$DBDR"
    "$EXE/getTargetsDef" "$DBDR/.$DB.fileToTaxIDs" $RANK >> "$DBDR/targets.txt"
    popd
fi
echo "-T $DBDR/targets.txt" > "$DBDR/.settings"
if [ ! -d "$DBDR/$DB" ]; then
    echo "Creating directory to store discriminative k-mers: $DBDR/$DB"
    mkdir -m 775 "$DBDR/$DB"
fi
echo "-D $DBDR/$DB/" >> "$DBDR/.settings"