centerSelect/centerSelect.sh at master · WillyBruhn/centerSelect · GitHub

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#!/bin/bash

parametersFile="./parameters.txt"
if [ $# -eq 0 ]
  then
    echo "No arguments supplied ..."
else
	parametersFile=$1
fi

echo "reading in parameters from $parametersFile"

echo "found the following parameters..."
echo "paramameter          value"
NLS="-----------------------------------------------------------"
echo $NLS
#-----------------------------------------------------------------------------------
IFS=";"
while read parameter value
do
    echo "$parameter              $value"

	if [ "$parameter" == "path2centerSelect" ]; then
		path2centerSelect=$value

	elif [ "$parameter" == "path2files" ]; then
		path2files=$value

	elif [ "$parameter" == "boxSize" ]; then
		boxSize=$value


	elif [ "$parameter" == "depth" ]; then
		depth=$value


	elif [ "$parameter" == "eps" ]; then
		eps=$value


	elif [ "$parameter" == "eps" ]; then
		eps=$value


	elif [ "$parameter" == "onlyDoMissing" ]; then
		onlyDoMissing=$value

	elif [ "$parameter" == "path2output" ]; then
		path2output=$value

    elif [ "$parameter" == "SELECTBOX" ]; then
		SELECTBOX=$value

	else
		echo "corrupted format in $parametersfile/parameters.txt"
		echo "aborting ..."
		exit
	fi

done < $parametersFile
echo $NLS

cp $parametersFile $path2files/$parametersFile
#-----------------------------------------------------------------------------------

#path2centerSelect="/home/willy/RedoxChallenges/centerSelect/"
#path2files="/home/willy/RedoxChallenges/centerSelect/Redox_old/Output/"
#boxSize=30
#
## point[3] > center[3] - depth; positive depth means more points
#depth=10
#eps=0.3

function selectCenter {
	d=$1

	echo $d
	echo $filename

    filename="${d%/}"

	f="$path2output/$filename/$filename"

	rm "$f""HeadOff.pqr"

	sed '1,1d' "$f.pqr"  >> $f."tmp.pqr"
	sed '$d' $f."tmp.pqr"  >> "$f""HeadOff.pqr"

	rm $f."tmp.pqr"


	$path2centerSelect/./centerSelecter.R $path2centerSelect $path2output $filename $boxSize $depth $eps $SELECTBOX
}


#missingList=$($path2centerSelect./WhichMissing.sh $path2files)


#while read -r line; do
#    echo "... $line ..."
#done <<< "$missingList"

#exit

if [ $path2output != "false" ]; then
	echo "copying files from $path2files to $path2output ..."
	cp -r $path2files $path2output

else
	echo "using original files in $path2files ..."
	path2output=$path2files
fi

cd $path2output

#for d in */ ; do

echo "onlyDoMissing == $onlyDoMissing ..."

if [ $onlyDoMissing == true ]; then

	echo "... performing only for missing folders"

	missingList=$($path2centerSelect./WhichMissing.sh $path2output)

	while read -r d; do (
		selectCenter $d
    ) #&
	done <<< "$missingList"

	#wait
else

	echo "... performing for all folders"

	for d in */ ; do (
		selectCenter $d
    ) #&
	done

	#wait
fi


echo $NLS
#-----------------------------------------------------------------------------------
echo $path2output
echo "still missing active centers of ..."
missing=$($path2centerSelect./WhichMissing.sh $path2output)
echo $missing

cd $path2centerSelect
echo "$missing" > "missing.txt"