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Suggestion: parallelize low complexity masking #39

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Suggestion: parallelize low complexity masking #39

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582338f
Suggestion: parallelize repeat masking
tskir Aug 11, 2018
c621b4c
Do not keep order during parallelization
tskir Aug 11, 2018
62f2eb2
Fix error when passing $MASKER variable
tskir Aug 12, 2018
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13 changes: 11 additions & 2 deletions scripts/mask_low_complexity.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -23,17 +23,26 @@ if ! which $MASKER > /dev/null; then
exit 1
fi

function mask_data_chunk () {
# Removes empty records and performs masking, all in pipes
MASKER=$1
awk -v RS=">" -v FS="\n" -v ORS="" ' { if ($2) print ">"$0 } ' |\
$MASKER -in - -outfmt fasta |\
sed -e '/^>/!s/[a-z]/x/g'
}
export -f mask_data_chunk

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"
cat $file | parallel --pipe --recstart '>' --blocksize 100M mask_data_chunk $MASKER > "$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"
cat $target | parallel --pipe --recstart '>' --blocksize 100M mask_data_chunk $MASKER > "$target.tmp"
mv "$target.tmp" $target
touch "$target.masked"
fi
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