04.run_cluster.sh

#!/bin/bash
#pipeline 4
if [ ! -n "$3" ]
then
	#Usage
	echo "	Part 4: clustering reads"
	echo "	Single flnc.bam file or list all flnc.bam to flnc.fnfo"
	echo "	Usage: bash `basename $0` [flnc.bam|flnc.fnfo] [OutputPrefix] [threads]"
	echo "	Example: bash `basename $0` JJ27_Tes.ccs.fl.*Clonetech_3p.flnc.bam JJ27_Tes 2"
	echo "	Output: clustered reads [OutputPrefix.ccs.flnc.clustered.bam]"
else
	#Processing
	data=$1
	prefix=$2
	threads=$3
	echo "`basename $0`"
	echo ">>Starting the pipeline to cluster reads"
	echo "	Input data: "$data
	echo "	OutPrefix: "$prefix
	st=`date`
	isoseq3 cluster $data ${prefix}.ccs.flnc.clustered.bam --use-qvs --num-threads $threads
	gunzip ${prefix}.ccs.flnc.clustered.hq.fasta.gz
	gunzip ${prefix}.ccs.flnc.clustered.lq.fasta.gz
	ed=`date`
	bn=`samtools view $data|grep -v "^@"|wc -l`
	an=`samtools view ${prefix}.ccs.flnc.clustered.bam|grep -v "^@"|wc -l`
	echo "**Statistical**"
	echo "Before cluster: "$bn
	echo "After cluster: "$an
	echo "Started time: "$st
	echo "Ended time: "$ed
	echo "Done running `basename $0`"
	echo "**********************************************************************************"
fi