#!/bin/sh

# fastaSubseq - shell script to replace the fasta-subseq command from
#	ancient blastz source - using nibFrag and faFrag to reproduce the
#	same behavior.  Almost, doesn't honor negative strand fasta files,
#	will error out in that case.

set -beEu -o pipefail

if [ $# -lt 3 -o $# -gt 4 ]; then
    echo "usage: fastaSubseq seqfile lo hi [strand] (1 indexed)" 1>&2
    exit 255
fi
export file=$1
export start=$2
export end=$3
export strand="+"

if [ $# -eq 4 ]; then
    strand=$4
fi

if [ $start -lt 1 ]; then
    echo "ERROR: fastaSubseq: start coordinate can not be less than zero: '$start'" 1>&2
    exit 255
fi

export sequenceName="${file}:${start}-${end}:___"

export startZero=`echo $start | awk '{print $1-1}'`

case $file in
    *nib) nibFrag -name="$sequenceName" -masked \
	$file $startZero $end $strand stdout ;;
    *fa)
	if [ $strand != "+" ]; then
	    echo "ERROR: fastaSubseq: sorry, can only work with strand +, given: '$strand'" 1>&2
	    exit 255
	fi
	faFrag -mixed $file $startZero $end stdout \
	    | sed -e "s/^>.*/>$sequenceName/" ;;
    *) echo "ERROR: fastaSubseq: can not recognize input file as .nib or .fa, given:" 1>&2
	echo $file 1>&2
	exit 255
	;;
esac