metaspectrast

#!/usr/bin/env bash
# Hao, Chunlin@20220506

VERSION=0.0
PIPES=$(dirname $(which metaspectrast))/bin

help_msg () {
	echo "_________ metaSpectraST by Hao, Chunlin _________"
	echo ""
	echo "metaSpectraST v=${VERSION}"
	echo "Usage: metaspectrast [module]"
	echo ""
	echo "Module:"
	echo "1  cluster          Clustering MS/MS spectra and create consensus spectra"
	echo "2  computesc        Spectral count-based (SC) sample profiling"
	echo "3  computesin       Normalized spectral index (SIn) based sample profiling"
	echo "4  normalize        Normlizing the data matrix of sample profiles (SC or SIn)"
	echo "5  classify         Hierarchically clustering and classifying samples"
	echo "6  reconcile        Reconciliation scheme"
}


if [ "$1" = cluster ]; then
	${PIPES}/runSpectraST.sh ${@:2}
elif [ "$1" = computesc ]; then
	python ${PIPES}/metaSpectraST_SC.py ${@:2}
elif [ "$1" = computesin ]; then
	python ${PIPES}/metaSpectraST_SIn.py ${@:2}
elif [ "$1" = normalize ]; then
	python ${PIPES}/normalization.py ${@:2}
elif [ "$1" = classify ]; then
	python ${PIPES}/hierarchy_heatmap.py ${@:2}
elif [ "$1" = reconcile ]; then
	python ${PIPES}/vote_consensusPep.py ${@:2}
elif [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
	help_msg
	exit 0
elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
	echo "metaSpectraST v${VERSION} by Hao, Chunlin"
	exit 0
else
	echo "Please select a proper module of metaSpectraST."
	echo ""
	help_msg
	exit 1
fi