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#! /bin/sh
# Sort MAF-format alignments by sequence name, then start position,
# then end position, of the top sequence. Also, merge identical
# alignments. Comment lines starting with "#" are written at the top,
# in unchanged order. If option "-d" is specified, then alignments
# that appear only once are omitted (like uniq -d).
# Maybe the sorting should consider the strand of the top sequence?
# XXX Preceding whitespace is considered part of the sequence name. I
# want to use sort -b, but it seems to be broken in different ways for
# different versions of sort!
# XXX Alignments with differences in whitespace are considered
# non-identical.
# This script uses perl instead of specialized commands like uniq.
# The reason is that, on some systems (e.g. Mac OS X), uniq doesn't
# work with long lines.
# Make "sort" use a standard ordering:
LC_ALL=C
export LC_ALL
uniqOpt=1
while getopts hd opt
do
case $opt in
h) cat <<EOF
Usage: $(basename $0) [options] my-alignments.maf
Options:
-h show this help message and exit
-d only print duplicate alignments
EOF
exit
;;
d) uniqOpt=2
;;
esac
done
shift $((OPTIND - 1))
tmpfile=${TMPDIR-/tmp}/maf-sort.$$
cat "$@" | tee $tmpfile | perl -ne 'print if /^#/'
perl -ne 'print unless /^#/' $tmpfile | # remove comment lines
perl -pe 'y/ /!/ if /^a/' | # change spaces to '!'s in 'a' lines
perl -pe 's/\n/#/ if /\S/' | # join each alignment into one big line
sort -k2,2 -k3,3n -k4,4n | # sort the lines
# print only the first (or second) of each run of identical lines:
perl -ne '$c = 0 if $x ne $_; $x = $_; print if ++$c == '$uniqOpt |
perl -pe 's/#/\n/g' | # undo the line-joining
perl -pe 'y/!/ / if /^a/' # change '!'s back to spaces in 'a' lines
rm $tmpfile
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