/usr/bin/paraclu-cut.sh is in paraclu 9-1+b2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | #! /bin/sh
# Copyright 2011, 2012 Martin C. Frith
# This script simplifies the output of paraclu. It omits clusters
# that are too long, or are singletons. Then, it removes clusters
# whose fold-increase in density is too small. Finally, it removes
# clusters that are contained in larger clusters.
# This script assumes that the input is sorted by start position
# (ascending) then end position (descending).
maxLengthDefault=200
minDensityRiseDefault=2
maxLength=$maxLengthDefault
minDensityRise=$minDensityRiseDefault
isSingleClusterIncrease=
while getopts hl:d:s opt
do
case $opt in
h) cat <<EOF
Usage: $(basename $0) [options] [paraclu-output-file(s)]
Extract a subset of clusters from the output of paraclu.
Options:
-h show this help message and exit
-l maximum cluster length (default $maxLengthDefault)
-d minimum density increase (default $minDensityRiseDefault)
-s density increase applies to single clusters, not cumulatively
EOF
exit
;;
l) maxLength=$OPTARG
;;
d) minDensityRise=$OPTARG
;;
s) isSingleClusterIncrease=1
;;
esac
done
shift $(($OPTIND - 1))
# Remove singleton clusters.
# Remove clusters longer than maxClusterLength.
awk '
$3 < $4 && $4 - $3 <= '$maxLength'
' "$@" |
if [ -n "$isSingleClusterIncrease" ]
then
# Remove clusters less stable than minDensityRise.
awk '$7 * '$minDensityRise' <= $8'
else
# Remove clusters whose density is insufficiently above the local
# baseline density.
awk '
{n = $1" "$2}
n != o {e=-1; o=n}
$4 > e {e=$4; s=$7}
s * '$minDensityRise' <= $8 {print}
'
fi |
# Remove clusters that are contained in larger clusters.
awk '
{n = $1" "$2}
n != o {e=-1; o=n}
$4 > e {print; e=$4}
'
|