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getTargetsKmers_distribution.sh
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#! /bin/sh
#
# CLARK, CLAssifier based on Reduced K-mers.
#
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright @ The Regents of the University of California. All rights reserved.
#
#
#
# @author: Rachid Ounit, Ph.D.
# @project: CLARK, Metagenomic and Genomic Sequences Classification project.
# @note: C++/Shell IMPLEMENTATION supported on latest Linux and Mac OS.
# getTargetsKmers_distribution.sh: To estimate abundance of target identified (reported
# by taxa name and lineage) with count and proportion
# (against all reads or classified reads).
# Filtering options are offered.
#
FSCRPT=$(readlink -f "$0")
LDIR=$(dirname "$FSCRPT")
if [ $# -lt 2 ]; then
echo "Usage: $0 <k-mer length: integer between 2 and 32> <min k-mers frequency: default is 0>"
exit
fi
$LDIR/exe/getTargetSpecificKmersStat $LDIR/.settings $@