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#!/bin/bash
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
# Masks low complexity sequences in the database using the dustmasker (nucl.)
# or segmasker (prot.) programs from NCBI.
set -u # Protect against uninitialized vars.
set -e # Stop on error
set -o pipefail # Stop on failures in non-final pipeline commands
target="$1"
MASKER="k2mask"
if [ -n "$KRAKEN2_PROTEIN_DB" ]; then
MASKER="segmasker"
fi
if ! which $MASKER > /dev/null; then
echo "Unable to find $MASKER in path, can't mask low-complexity sequences"
exit 1
fi
if [ -d $target ]; then
for file in $(find $target '(' -name '*.fna' -o -name '*.faa' ')'); do
if [ ! -e "$file.masked" ]; then
$MASKER -in $file -outfmt fasta | sed -e '/^>/!s/[a-z]/x/g' > "$file.tmp"
mv "$file.tmp" $file
touch "$file.masked"
fi
done
elif [ -f $target ]; then
if [ ! -e "$target.masked" ]; then
$MASKER -in $target -outfmt fasta | sed -e '/^>/!s/[a-z]/x/g' > "$target.tmp"
mv "$target.tmp" $target
touch "$target.masked"
fi
else
echo "Target $target must be directory or regular file, aborting masking"
exit 1
fi
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