05.run_gmap.sh

#!/bin/bash
#Considering splicing
if [ ! -n "$3" ]
then
	echo "	Part 5: Mapping hq/lq cluster to genome"
	echo "	Usage: bash `basename $0` [*.ccs.flnc.clustered.hq.fasta] [db_name] [threads]"
	echo "		<db_name> if no db_name, use 'gmap_build -d db_name genome.fa' to build it"
	echo "	Example: bash `basename $0` JJ27_Tes.ccs.flnc.clustered.hq.fasta ssc_ens107db 2"
	echo "	Output: sorted sam file [*.ccs.flnc.clustered.hq.fasta.db_name.sorted.sam]"
else
	#-n 1 will not report chimeric
	data=$1
	db=$2
	threads=$3
	if [[ -e $data ]]
	then
		echo "`basename $0`"
		echo ">>Starting genome mapping by gmap"
		echo "  Input data: "$data
		echo "  Using db: "$db
		echo "  Only mapped reads will be reported"
		st=`date`
		gmap.sse42 -d $db -t $threads -B 5 -A -f samse --nofails -n 1 $data 1>${data}.${db}.sam 2>${data}.${db}.log && \
			sort -k 3,3 -k 4,4n ${data}.${db}.sam > ${data}.${db}.sorted.sam && \
			rm ${data}.${db}.sam
		bn=`less $data|grep ">"|wc -l`
		an=`less ${data}.${db}.sorted.sam|grep -v "^@"|wc -l`
		ed=`date`
		echo "	**Summary:"
		echo "Input reads: "$bn
		echo "Mapped reads: "$an
		echo "Started time: "$st
		echo "Ended time: "$ed
		echo "Done running `basename $0`"
		echo "**********************************************************************************"
	else
		echo "No such file: "$data
	fi
fi