#!/bin/bash
# mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
if [ "" == "$MGESCAN_SRC" ]
then
	echo "\$MGESCAN_SRC is not defined."
	exit
fi

script_program=`which python`
script=$MGESCAN_SRC/mgescan/cmd.py
input_file=$1
#input_file_name=$2
input_file_name=`basename $input_file`
hmmsearch_version=$3
output_file=$4
program=$5 # N is nonLTR, L is LTR and B is both
# Optional output parameters for nonLTR
clade=$6
en=$7
rt=$8
ltr_gff3=$9
nonltr_gff3=${10}
both_gff3=${11}
#### for ltr between $11 and $20
if [ "$program" == "L" ]
then
	sw_rm=${12}
	scaffold=${13}
	min_dist=${14}
	max_dist=${15}
	min_len_ltr=${16}
	max_len_ltr=${17}
	ltr_sim_condition=${18}
	cluster_sim_condition=${19}
	len_condition=${20}
	repeatmasker=${21}
fi

#elif [ "$program" == "B" ]
if [ $# -eq 12 ]
then
	nmpi=${12}
	if [ ! -z $nmpi ] && [ $nmpi -ge 1 ]
	then
		mpi_enabled="--mpi=$nmpi"
	fi

fi

# /nfs/nfs4/home/lee212/mgescan/galaxy-dist/tools/mgescan/find_ltr.sh /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_1.dat /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_3.dat

#set path for transeq
#export PATH=$user_dir/mgescan/EMBOSS/bin:/usr/bin:$PATH
transeq --version 2> /dev/null
res=$?
if [ 0 -ne $res ]
then
	echo "EMBOSS is not available."
	exit
fi

#move to the working directory
work_dir=`dirname $script`
cd $work_dir

#create directory for input and output
mkdir -p input
t_dir=`mktemp -p input -d` #relative path
input_dir="$work_dir/$t_dir/seq" # full path
output_dir="$work_dir/$t_dir/data"
mkdir -p $input_dir
mkdir -p $output_dir

#make a copy of input
#/bin/cp $input_file $input_dir/$input_file_name

# Check tar.gz
tar tf $input_file &> /dev/null
ISGZ=$?
if [ 0 -eq $ISGZ ]
then
	# It seems pre_process.pl creates ./data/genome directory and makes a copy of a genome file.
	# Due to this reason, extracts compressed inputs to output directory.
	tar xzf $input_file -C $input_dir 2> /dev/null
	if [ $? -ne 0 ]
	then
		tar xf $input_file -C $input_dir 2> /dev/null
	fi
else
	/bin/ln -s $input_file $input_dir/$input_file_name
fi

VERSION2=`hmmsearch -h|grep "HMMER 2" 2> /dev/null`
VERSION3=`hmmsearch -h|grep "HMMER 3" 2> /dev/null`
if [ "2" == "$hmmsearch_version" ] && [ "" != "$VERSION2" ]
then
	echo $VERSION2 selected.
elif [ "3" == "$hmmsearch_version" ] && [ "" != "$VERSION3" ]
then
	echo $VERSION3 selected.
else
	echo HMMER is not available.
	exit
fi

if [ "$program" == "L" ]
then
	program_name="ltr"
elif [ "$program" == "N" ]
then
	program_name="nonltr"
else
	program_name="both"
fi

#run
$script_program $script $program_name $input_dir/ --output=$output_dir/ $mpi_enabled #-hmmerv=$hmmsearch_version -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}
#/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}

#RES=`ssh -i $user_dir/.ssh/.internal silo.cs.indiana.edu "/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program > /dev/null"`

#make a copy of output
if [ "$program" != "N" ]
then
	/bin/cp $output_dir/ltr/ltr.out $output_file
	if [ "$ltr_gff3" != "None" ]
	then
		/bin/cp $output_dir/ltr/ltr.gff3 $ltr_gff3
	fi

	if [ "$repeatmasker" != "None" ] && [ "$repeatmasker" != "" ]
	then
		# chr2L.fa.cat.gz  chr2L.fa.masked  chr2L.fa.out  chr2L.fa.out.pos  chr2L.fa.tbl
		/bin/cp $output_dir/repeatmasker/${input_file_name}.out $repeatmasker
	fi
fi
if [ "$program" != "L" ]
then

	tmp=`mktemp`
	RANDOM=`basename $tmp`
	compressed_file=$output_dir/$RANDOM.tar.gz
	/bin/tar czfP $compressed_file $output_dir/info
	#/bin/cp $compressed_file $output_file
	#RES=`/bin/cp $output_dir/info/full/*/* $clade 2> /dev/null`
	RES=`/bin/cp $compressed_file $clade 2> /dev/null`
	RES=`/bin/cp $output_dir/info/validation/en $en 2> /dev/null`
	RES=`/bin/cp $output_dir/info/validation/rt $rt 2> /dev/null`
	if [ "$nonltr_gff3" != "None" ]
	then
		/bin/cp $output_dir/info/nonltr.gff3 $nonltr_gff3
		# nonltr.gff3
		##gff-version 3
		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  19670384        19676921        .       .       .       ID=chr2L.fa_19670384
		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  17689430        17695994        .       .       .       ID=chr2L.fa_17689430
		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  11897186        11903717        .       .       .       ID=chr2L.fa_11897186
		#chr2L.fa        MGEScan_nonLTR  mobile_genetic_element  49574   56174   .       .       .       ID=chr2L.fa_49574
	fi

#else
	# Both LTR, nonLTR executed
	#compressed_file=$output_dir/$RANDOM.tar.gz
	#/bin/tar czfP $compressed_file $output_dir
	#/bin/cp $compressed_file $output_file
fi

if [ "$program" == "B" ]
then
	#echo "track name=LTR description=\"MGEScan-LTR\" color=0,0,255," > $both_gff3
	/bin/cat $output_dir/ltr/ltr.gff3 >> $both_gff3
	#echo "track name=nonLTR description=\"MGEScan-nonLTR\" color=255,0,0" >> $both_gff3
	/bin/cat $output_dir/info/nonltr.gff3 >> $both_gff3
fi

# delete temp directory
if [ $? -eq 0 ]
then
	rm -rf $work_dir/$t_dir
	#echo
else
	#echo cp -pr $work_dir/$t_dir $work_dir/error-cases/
	cp -pr $work_dir/$t_dir $work_dir/error-cases/
fi