count_fastq_sequences.sh

#!/bin/bash
if [ $# -lt 1 ] ; then
    echo ""
    echo "usage: count_fastq.sh [fastq_file1] <fastq_file2> ..|| *.fastq"
    echo "counts the number of reads in a fastq file"
    echo ""
    exit 0
fi
 
filear=${@};
for i in ${filear[@]}
do
lines=$(wc -l $i|cut -d " " -f 1)
count=$(($lines / 4))
echo -n -e "\t$i : "
echo "$count"  | \
sed -r '
  :L
  s=([0-9]+)([0-9]{3})=\1,\2=
  t L'
done