Chris@0: #!/bin/bash
Chris@0: 
Chris@0: if [ $# -lt 2 ] ; then
Chris@0: echo "Usage: $0 [-s] LISTFILENAME OUTPUTDIR"
Chris@0: exit 1
Chris@0: fi
Chris@0: 
Chris@0: retainstructure=0
Chris@0: 
Chris@0: while [ $# -gt 2 ] ; do
Chris@0: case $1 in
Chris@0: -d) retainstructure=1 ; shift 1 ; echo here;;
Chris@0: *) shift 1 ;;
Chris@0: esac
Chris@0: done
Chris@0: 
Chris@0: listfile="$1"
Chris@0: echo listfile "$listfile"
Chris@0: outputdir="$2"
Chris@0: 
Chris@0: 
Chris@0: while read infile; do
Chris@0: 	if [ "$infile" -a -f "$infile" ]; then
Chris@0: 		before="$(date +%s)"
Chris@0: 		echo "_____________________________________________________"
Chris@0: 		echo " "
Chris@0: 		echo Processing file "$infile"
Chris@0: 		echo " "
Chris@0: 		if [ $retainstructure -eq 0 ]; then
Chris@0: 			pathandfile=`basename "$infile"`
Chris@0: 		else
Chris@0: 			pathandfile="`echo "$infile" | egrep -o '[^/]*/[^/]*/[^/]*$'`"
Chris@0: 			echo pathandfile "$pathandfile"
Chris@0: 		fi
Chris@0: 		outfile="$outputdir"/"$pathandfile".txt
Chris@0: 		
Chris@0: 		logfile=_logfiles/"$pathandfile".log
Chris@0: 		chromafile=_chromadata/"$pathandfile".csv
Chris@0: 		
Chris@0: 		mkdir -p "`dirname "$outfile"`"
Chris@0: 		
Chris@0: 		echo "[sonic annotator] ..."
Chris@0: 		VAMP_PATH=. ./sonic-annotator -d vamp:matthiasm:nnls_chroma:bothchroma -w csv --csv-stdout "$infile" 2> "$logfile" | cut -d ',' -f 2-  > "$chromafile" 
Chris@0: 		infile="`echo "$infile" | sed "s/'/''/g"`"
Chris@0: 		outfile="`echo "$outfile" | sed "s/'/''/g"`"
Chris@0: 		chromafile="`echo "$chromafile" | sed "s/'/''/g"`"		
Chris@0: 		matlab -nodisplay -nojvm -r run_segmentation\(\'"$infile"\',\'"$outfile"\'\,\'"$chromafile"\'\) >> "$logfile"
Chris@0: 		after="$(date +%s)"
Chris@0: 		elapsed_seconds="$(expr $after - $before)"
Chris@0: 		echo "  -->" time elapsed: $elapsed_seconds seconds
Chris@0: 		echo " "
Chris@0: 	else if [ ! "$infile" ]; then echo ...; fi
Chris@0: 	fi		
Chris@0: done < "$listfile"