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#! /bin/sh
# This script reads MAF-format alignments with lastal header
# information, removes "uninteresting" alignments, and writes the
# remainder. Specifically, it removes alignments that are "dominated"
# in both genomes. See last-remove-dominated.py for the definition of
# "dominated". This procedure is likely to remove many paralogs, and
# it is unlikely to remove one-to-one orthologs.
# If option "-d" is specified, then it removes alignments that are
# dominated in either genome.
sortOpt=
while getopts hd opt
do
case $opt in
h) cat <<EOF
Usage: $(basename $0) [options] last-output.maf
Options:
-h show this help message and exit
-d reduce alignments more aggressively
EOF
exit
;;
d) sortOpt="-d"
;;
esac
done
shift $((OPTIND - 1))
PATH=$PATH:$(dirname $0) # assume the other scripts are in the same directory
{
# remove alignments that are dominated in the upper sequence
maf-sort.sh "$@" |
last-remove-dominated.py
# remove alignments that are dominated in the lower sequence
maf-swap.py "$@" |
maf-sort.sh |
last-remove-dominated.py |
maf-swap.py
} | maf-sort.sh $sortOpt # merge the results
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