Mauch MIREX 2010

#!/bin/bash

if [ $# -lt 2 ] ; then

echo "Usage: $0 [-s] LISTFILENAME OUTPUTDIR"

exit 1

fi

retainstructure=0

while [ $# -gt 2 ] ; do

case $1 in

-d) retainstructure=1 ; shift 1 ; echo here;;

*) shift 1 ;;

esac

done

listfile="$1"

echo listfile "$listfile"

outputdir="$2"

while read infile; do

	if [ "$infile" -a -f "$infile" ]; then

		before="$(date +%s)"

		echo "_____________________________________________________"

		echo " "

		echo Processing file "$infile"

		echo " "

		if [ $retainstructure -eq 0 ]; then

			pathandfile=`basename "$infile"`

		else

			pathandfile="`echo "$infile" | egrep -o '[^/]*/[^/]*/[^/]*$'`"

			echo pathandfile "$pathandfile"

		fi

		outfile="$outputdir"/"$pathandfile".txt

		logfile=_logfiles/"$pathandfile".log

		chromafile=_chromadata/"$pathandfile".csv

		mkdir -p "`dirname "$outfile"`"

		echo "[sonic annotator] ..."

		VAMP_PATH=. ./sonic-annotator -d vamp:matthiasm:nnls_chroma:bothchroma -w csv --csv-stdout "$infile" 2> "$logfile" | cut -d ',' -f 2-  > "$chromafile"

		infile="`echo "$infile" | sed "s/'/''/g"`"

		outfile="`echo "$outfile" | sed "s/'/''/g"`"

		chromafile="`echo "$chromafile" | sed "s/'/''/g"`"

		matlab -nodisplay -nojvm -r run_segmentation\(\'"$infile"\',\'"$outfile"\'\,\'"$chromafile"\'\) >> "$logfile"

		after="$(date +%s)"

		elapsed_seconds="$(expr $after - $before)"

		echo "  -->" time elapsed: $elapsed_seconds seconds

		echo " "

	else if [ ! "$infile" ]; then echo ...; fi

	fi

done < "$listfile"