fastq-read-count-and-validate.sh

#!/usr/bin/env sh
# Count reads and validate FASTQ files

FASTQ_DIR="$1"

if [ -z ${FASTQ_DIR+x} ]; then
    echo "Usage: $0 /path/to/fastq/files/"
    exit 1
fi

echo -e "FILE\tLINES\tREADS" >> $FASTQ_DIR/counts
for FQ in $FASTQ_DIR/*.fastq.gz; do

    LINES=`gunzip -c $FQ | wc -l`
    READS=$((LINES / 4))
    RECORD="$FQ\t$LINES\t$READS"

    # Warn if file is not a multiple of 4 lines
    if (( $LINES % 4 != 0 )); then
        RECORD="$RECORD\tERROR: Truncated File Detected"
    fi

    echo -e $RECORD >> $FASTQ_DIR/counts

done

fda-fastq-read-count-and-validate.sh

cd /bio/amaryllis/girihlet/fda/final-to-send/fq

echo -e "FILE\tLINES\tREADS" > ../counts
for FQ in *.fq.gz  *.fastq.gz; do

    LINES=`gunzip -c $FQ | wc -l`
    READS=$((LINES / 4))
    RECORD="$FQ\t$LINES\t$READS"

    # Warn if file is not a multiple of 4 lines
    if (( $LINES % 4 != 0 )); then
        RECORD="$RECORD\tERROR: Truncated File Detected"
    fi

    echo -e $RECORD >> ../counts

done &