replong.sh

#! /bin/bash
SECONDS=0
DIR=$( cd $(dirname $0) ; pwd -P )
printf "script path = %s\n" $DIR
#source ${DIR}/generateFasta.sh
source ${DIR}/processRead.sh 
lines=65000000 genomeSize= file= temp= lendiff=200 fromlen=250 ratio=0.96 drops=3 n1=3 n2=8 degree=10 commu_size=10 window=100 cor=false breaks=200 outputfile="replong.log" canuPath="" faidxPath="" javaPath="" minOverlapLength=500 minReadLength=1000 netMinOverlap=100 weight=false
while getopts f:o:r:s:e:h:n:l:t:p:j:b:q:w:d:x:c:g:a:m:z: opt
do
	case $opt in
		f)	file=$OPTARG
			;;
		s)	genomeSize=$OPTARG
			;;
		h)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))
			continue
			fi
			maxThreads=$OPTARG
			;;
		e)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))
			continue
			fi
			maxMemory=$OPTARG
			;;
		r)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))
			continue
			fi
			minReadLength=$OPTARG
			;;
		o)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))
			continue
			fi
			minOverlapLength=$OPTARG
			;;
		j)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			javaPath=$OPTARG
			;;
		l)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			lines=$OPTARG
			;;
		t)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			temp=$OPTARG
			;;
		b)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			breaks=$OPTARG
			;;
		x)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			drops=$OPTARG
			;;
		q)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			n1=$OPTARG
			;;
		w)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			weight=$OPTARG
			;;
		p)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			netMinOverlap=$OPTARG
			;;
		y)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			n2=$OPTARG
			;;
		d)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			degree=$OPTARG
			;;
		a)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			faidxPath=$OPTARG
			;;
		g)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			lendiff=$OPTARG
			;;
		c)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			cor=$OPTARG
			;;
		m)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			fromlen=$OPTARG
			;;
		z)	if [[ $OPTARG = -* ]]; then
			((OPTIND--))  
			continue
			fi
			outputfile=$OPTARG
	esac
done
shift $((OPTIND - 1))
printf "file=%s\n" $file 
printf "genomeSize=%s\n" $genomeSize 
#printf "range=%s\n"	$range 
printf "correction=%s\n" $cor 
#printf "lines=%s\n" $lines 
printf "temp folder=%s\n" ${temp}
#printf "breaks=%d\n" ${breaks} 
#printf "n1=%d\n" $n1
#printf "n2=%d\n" $n2
#printf "degree=%d\n" $degree
#printf "commu_size=%d\n" $commu_size
#printf "drops=%d\n" $drops
printf "lendiff=%d\n" $lendiff
#printf "ratio=%s\n" $ratio
#printf "window=%d\n" $window
printf "fromlen=%d\n" $fromlen
printf "outputfile=%s\n" $outputfile
printf "network minimum overlap length=%s\n" $netMinOverlap
home=$(pwd)
orifile="$(cd "$(dirname "$file")" && pwd)/$(basename "$file")"
printf "original place=%s\n" $home

if [ -z $file ]
then
printf "no input file!\n"
exit 1
fi

if [ -z $temp ]
then
printf "no temp folder!\n"
exit 1
fi

if [ -z $genomeSize ]
then
printf "no genome size!\n"
exit 1
fi

mkdir $temp
if [ -z $javaPath ]
then
	javaPath=$(command -v java)	
	javaPath=${javaPath%java}
else
	ORGPATH=`pwd`
	RELPATH=$javaPath
	cd $RELPATH
	javaPath=`pwd`
	cd $ORGPATH
fi

#if [ -z $canuPath ]
#then
#        canuPath=$(command -v canu)
#        canuPath=${canuPath%canu}
#else
#        ORGPATH=`pwd`
#	canuPath=${canuPath%canu}
#        RELPATH=$canuPath
#        cd $RELPATH
#        canuPath=`pwd`
#        cd $ORGPATH
#fi
canuPath="canu/Linux-amd64/bin"
canuPath="$DIR/$canuPath"

if [ -z $faidxPath ]
then
	faidxPath=$(command -v faidx)	
	faidxPath=${faidxPath%faidx}
else
	ORGPATH=`pwd`
	RELPATH=$faidxPath
	cd $RELPATH
	faidxPath=`pwd`
	cd $ORGPATH
fi

printf "canu path is %s\n" $canuPath
printf "min Read Length is %s\n" $minReadLength
printf "min Overlap Length is %s\n" $minOverlapLength
printf "faidx path is %s\n" $faidxPath
printf "java path is %s\n" $javaPath
if [ $cor = true ]
then
	
	printf "Use raw reads, read correction is running.\n"
	$canuPath/canu -correct -p "step1" -d $temp genomeSize="$genomeSize"  saveReadCorrections=T maxThreads=$maxThreads maxMemory=$maxMemory java=$javaPath/java corOutCoverage=400 gnuplotTested=true minReadLength=$minReadLength minOverlapLength=$minOverlapLength corMinCoverage=0 -pacbio-raw "$file"
	printf "the folder is %s\n" $temp
	cd $temp
	printf "process reads\n"
	processRead
else
	printf "Use corrected reads, no need for read correction.\n"
	$canuPath/canu -correct -p "step1" -d $temp genomeSize="$genomeSize" corOutCoverage=400 java=$javaPath/java gnuplotTested=true maxThreads=$maxThreads maxMemory=$maxMemory corMinCoverage=0 minReadLength=$minReadLength minOverlapLength=$minOverlapLength  stopAfter=overlap -pacbio-corrected "$file"
	printf "the folder is %s\n" $temp
	cd $temp
	printf "process reads\n"
	processRead
fi	
#echo $parameters >> ${home}/${outputfile}
duration=$SECONDS
echo "$(($duration / 60)) minutes and $(($duration % 60)) seconds elapsed." >> ${home}/${outputfile}
#rm -rf $temp
cd $home