A script to convert a gzipped FASTQ file in Solexa 1.3+ quality offset (QUAL+64 encoding) to a FASTQ with Phred/Sanger offset (QUAL+33 encoding).

rEncodeFASTQ.sh

#!/bin/bash
#
#$ -j y
#$ -v LD_LIBRARY_PATH
#
#######################################################
#      rEncodeFASTQ.sh
#
# A script to convert a gzipped FASTQ file in Solexa 1.3+ 
# quality offset (QUAL+64 encoding) to a FASTQ with
# Phred/Sanger offset (QUAL+33 encoding). 
#
# agalma requires unzipped QUAL+33 datasets
#
# requires fastqSol2Phred 
# (https://github.com/RobersonLab/fastqSol2Phred.git)
#
#######################################################

# PARSING THE  ARGUMENTS
usage() { echo "Usage: $0 [-o OUTDIR=.] [-s SUFFIX] [.fq.gz files]" ; exit 1; }
while getopts ":ho:s:" opt; do
	case $opt in
        	o)
                	OUTDIR=$OPTARG
                   	;;
		s)	
			SUFFIX=$OPTARG
			;;
		h)	
			usage
			;;
               \?)
                   	echo "Invalid option: -$OPTARG" 
		   	usage
                   	exit 1
			;;
                :)
                	echo "Option -$OPTARG requires an argument." 
			usage
                    	exit 1
                    	;;
          esac
done
shift $(( OPTIND - 1 ))

# Defining defaults if arguments were not parsed
if [ -z "$OUTDIR" ]; then OUTDIR=. ; fi
if [ -z "$SUFFIX" ]; then SUFFIX=_Q33.fq ; fi

# iterate over files
for i in "$@"
do
	if [ -f $i ];
	then
		#catch the name of the file without the path before the first dot (.fq.gz)
		F=$(echo $i | rev | cut -d'/' -f1 | rev | cut -d'.' -f1)
		# Check if the file was previously recoded, if not then do it!
		if [ ! -f $OUTDIR/$F$SUFFIX ]; 
		then 
			echo "recoding $i to Phred33 in $OUTDIR/$F$SUFFIX"
			#Execute the converter
			fastqSol2Phred <(gunzip -c $i) $OUTDIR/$F$SUFFIX
			gzip $OUTDIR/$F$SUFFIX
		else
			echo "$OUTDIR/$F$SUFFIX already exists! Next one, please!"
		fi;
	else
		echo "$i is not a file! Skipped!"
	fi;
done