short_read_connector.sh

#!/bin/bash

version="1.0.0"



EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
platform='mac'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
   platform='linux'
fi

dsk_bin=$EDIR/thirdparty/dsk/bin/macosx/dsk
if [[ $platform == 'linux' ]]; then
       dsk_bin=$EDIR/thirdparty/dsk/bin/linux/dsk
fi
chmod a+x ${dsk_bin}


#BIN DIR:
if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
       BIN_DIR=$EDIR/build/bin
else # VERSION BINARY
       BIN_DIR=$EDIR/bin
fi


function help {
echo "short_read_connector.sh - Groups reads within a RNA read set."
echo "Version "$version
echo "Usage: sh short_read_connector.sh -b read_file_of_files [OPTIONS]"
echo  "MANDATORY:"
echo  "	-b read_file_of_files for bank"
echo  "	  Example: -b data/c1.fasta.gz"

echo  "OPTIONS:"
echo  "	-p prefix. All out files will start with this prefix. Default=\"short_read_connector_res\""
echo  "	-g: with this option, if a file of solid kmer exists with same prefix name and same k value, then it is re-used and not re-computed."
echo  "	-k value. Set the length of used kmers. Must fit the compiled value. Default=31"
echo  "	-f value. Fingerprint size. Size of the key associated to each indexed value, limiting false positives. Default=12"
echo  "	-G value. gamma value. MPHF expert users parameter - Default=2"
echo  "	-a: kmer abundance min (kmer from bank seen less than this value are not indexed). Default=2"
echo  "	-s: Minimal percentage of shared kmer in a region for considering 2 reads in a same group. Default=75"
echo  " -w: Region (putative exon) size. Default=80"
echo  "	-t: number of thread used. Default=0"
echo  "	-d:  use disk over RAM (slower and no impact with -c option)"
echo  "	-c: use short_read_connector_counter (SRC_counter)"
echo  " -r: use short_read_connector_RNA (SRC_linker_RNA)"
}



bank_set=""
query_set=""
kmer_size=31
abundance_min=2
gamma=5
fingerprint_size=24
kmer_threshold=75
window_size=80
core_used=0
prefix="short_read_connector_res"
remove=1
diskMode=0
countMode=0

#######################################################################
#################### GET OPTIONS                #######################
#######################################################################
while getopts "hgb:q:p:k:a:s:w:t:f:G:dcr" opt; do
case $opt in

h)
help
exit
;;

G)
echo "use gamma: $OPTARG" >&2
gamma=$OPTARG
;;

d)
echo "use disk mode"
diskMode=1
;;

c)

echo "use SRC_counter"
countMode=1
;;


r)

echo "use SRC_linker_RNA"
rnaMode=1
;;


f)
echo "use fingerprint size: $OPTARG" >&2
fingerprint_size=$OPTARG
;;

b)
echo "use bank read set: $OPTARG" >&2
bank_set=$OPTARG
;;

q)
echo "use query read set: $OPTARG" >&2
query_set=$OPTARG
;;

p)
echo "use prefix=$OPTARG" >&2
prefix=$OPTARG
;;

g)
echo "reuse solid precomputed solid kmers if exists"
remove=0
;;

k)
echo "use k=$OPTARG" >&2
kmer_size=$OPTARG
;;


a)
echo "use abundance_min=$OPTARG" >&2
abundance_min=$OPTARG
;;

s)
echo "use kmer_threshold=$OPTARG" >&2
kmer_threshold=$OPTARG
;;

w)
echo "use window_size=$OPTARG" >&2
window_size=$OPTARG
;;


t)
echo "use $OPTARG threads">&2
core_used=$OPTARG
;;

       #
       # u)
       # echo "use at most $OPTARG cores" >&2
       # option_cores_gatb="-nb-cores $OPTARG"
       # option_cores_post_analysis="-t $OPTARG"
       # ;;

\?)
echo "Invalid option: -$OPTARG" >&2
exit 1
;;

:)
echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
#######################################################################
#################### END GET OPTIONS            #######################
#######################################################################

if [ -z "${bank_set}" ]; then
	echo "You must provide a bank read set (-b)"
help
exit 1
fi


out_dsk=${prefix}"_solid_kmers_k"${kmer_size}".h5"
result_file=${prefix}".txt"


if [ $remove -eq 1 ]; then
	rm -f ${out_dsk}
fi

# Count kmers using dsk if file absent
if [ ! -e ${out_dsk} ]; then
       cmd="${dsk_bin} -file ${bank_set} -kmer-size ${kmer_size} -abundance-min ${abundance_min} -out ${out_dsk} -solidity-kind all"
       echo ${cmd}
       ${cmd}
if [ $? -ne 0 ]
then
echo "there was a problem with the kmer counting."
exit 1
fi
fi
# Compare read sets


# SRC_LINKER_RNA
if [ $diskMode -eq 0 ]; then
	cmd="${BIN_DIR}/SRC_linker_rna"
	# adding options
	cmd="${cmd} -graph ${out_dsk}  -bank ${bank_set}  -out ${result_file} -kmer_threshold ${kmer_threshold} -window_size ${window_size} -fingerprint_size ${fingerprint_size} -core ${core_used} -gamma ${gamma}"

#else
	# SRC_LINKER_DISK
#	cmd="${BIN_DIR}/SRC_linker_disk"
	# adding options
#	cmd="${cmd} -graph ${out_dsk}  -bank ${bank_set} -query{query_set} -out ${result_file} -kmer_threshold ${kmer_threshold} -fingerprint_size ${fingerprint_size} -core ${core_used} -gamma ${gamma}"

fi

# adding options
#cmd="${cmd} -graph ${out_dsk}  -bank ${bank_set} -query ${query_set} -out ${result_file} -kmer_threshold ${kmer_threshold} -fingerprint_size ${fingerprint_size} -core ${core_used} -gamma ${gamma}"

echo ${cmd}
${cmd}
if [ $? -ne 0 ]
then
echo "there was a problem with short read connector."
exit 1
fi



# sort results
#sort -n ${unsorted_result_file} > ${result_file}


#rm -f ${unsorted_result_file}
./scripts/SRC_linker2reads.py ${bank_set} ${result_file}

echo "***********************************"
echo "Short read connector finished"
echo "results in:"
echo "   "${result_file}
echo "Contact: pierre.peterlongo@inria.fr"
echo "***********************************"