demultiplex_sabre.sh

#!/bin/bash

#######################################################################################
###                                                                                 ###
###     Copyright (C) 2017  Pawel Krawczyk (p.krawczyk@ibb.waw.pl)                  ###
###                                                                                 ###
###     This program is free software: you can redistribute it and/or modify        ###
###     it under the terms of the GNU General Public License as published by        ###
###     the Free Software Foundation, either version 3 of the License, or           ###
###     (at your option) any later version.                                         ###
###                                                                                 ###
###     This program is distributed in the hope that it will be useful,             ###
###     but WITHOUT ANY WARRANTY; without even the implied warranty of              ###
###     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               ###
###     GNU General Public License for more details.                                ###
###                                                                                 ###
###     You should have received a copy of the GNU General Public License           ###
###     along with this program. If not, see <http://www.gnu.org/licenses/>.        ###
###                                                                                 ###
#######################################################################################

#specify location of sabre:
sabre_script=`which sabre`
sabre_max_mismatches='2' # max number of mismatches allowed in primer/barcode

#get input dir from command line
input_dir=$1

#output dir
out_dir='processing_out_sabre'
#nmae of barcode files

# check if required software is accessible (in the PATH)
if ! [ -x "$(command -v $sabre_script)" ]; then
  echo 'Error: Sabre is not accessible.' >&2
  exit 1
fi

mkdir $out_dir


for R5_file in `find $input_dir -name '*R5.fastq'`
do
 echo "processing $R5_file"
 FILENAME_PREFIX=`expr match "$R5_file" '\(.*\)R5'`
 PREFIX_BASENAME=`expr match "$FILENAME_PREFIX" '.*\/\(.*\)'`
 R3_file=$FILENAME_PREFIX"R3.fastq"
 sabre_barcodes_file=$PREFIX_BASENAME"barcodes.txt"
 sabre_output=$PREFIX_BASENAME"sabre_out.txt" # this file will contain all demultiplex statistics
 output_R5_untrimmed=$out_dir'/'$PREFIX_BASENAME"R5_untrimmed.fastq" #location of untrimmed R5 reads
 output_R3_untrimmed=$out_dir'/'$PREFIX_BASENAME"R3_untrimmed.fastq"	#location of untrimmed R3 reads

 #perform demultiplexing
 $sabre_script pe -f $R5_file -r $R3_file -b $sabre_barcodes_file -u $output_R5_untrimmed -w $output_R3_untrimmed -m $sabre_max_mismatches > $sabre_output

done