Shell script for selecting fastq files by number of seqs.

remove_low_seq_files.sh

#!/usr/bin/env bash

if [ $# -eq 0 ] 
then
	echo "No arguments supplied..."
	echo "Please provide a minimum number of seqs per file."
	exit 1 
fi

MIN_LENGTH=$1
FILE_LIST=$(find . -type f -name "*.fastq" | sort)
declare -a BAD_FILE_LIST

echo -e "\nThe following files have passed QC (They will be copied with '.out'):"

for FILE in $FILE_LIST
do
	SEQ_COUNT=$(grep '^+' $FILE | wc -l)
	SEQ_DATA="$FILE	$SEQ_COUNT"
	
	if (("$SEQ_COUNT" < "$MIN_LENGTH"))
	then
		BAD_FILE_LIST+=("$SEQ_DATA")
	else
		echo "$SEQ_DATA"
		cp "$FILE" "$FILE.out"
	fi
done

echo -e "\nThe following files did not pass QC:"

for FILE in "${BAD_FILE_LIST[@]}"
do
	echo "$FILE" 
done

exit 0