File: compare-fastx

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file content (14 lines) | stat: -rwxr-xr-x 331 bytes parent folder | download | duplicates (6) 
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#!/bin/bash
set -eu -o pipefail

if [ $# -ne 2 ]; then
	echo "Usage: $(basename $0) <file1> <file2>" >&2
	echo "Compare FASTX files without regard for sequence orientation." >&2
	exit 1
fi

function canonical_seqs {
	bioawk -c fastx '{print $seq; print revcomp($seq)}' "$@" | sort
}

diff <(canonical_seqs $1) <(canonical_seqs $2)