#!/bin/sh

#
# Downloads sequence for the rn4 version of R. norvegicus (rat) from
# UCSC.
#
# Note that UCSC's rn4 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful.  To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# variable below.
#

i=2
BASE_CHRS=chr1
while [ $i -lt 21 ] ; do
	BASE_CHRS="$BASE_CHRS chr$i"
	i=`expr $i + 1`
done
BASE_CHRS="$BASE_CHRS chrX chrM chrUn"

RANDOM_CHRS="\
chr1_random \
chr2_random \
chr3_random \
chr4_random \
chr5_random \
chr6_random \
chr7_random \
chr8_random \
chr9_random \
chr10_random \
chr11_random \
chr12_random \
chr13_random \
chr14_random \
chr15_random \
chr16_random \
chr17_random \
chr18_random \
chr19_random \
chr20_random \
chrX_random \
chrUn_random"

CHRS_TO_INDEX=$BASE_CHRS

RN4_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/chromosomes

get() {
	file=$1
	if ! wget --version >/dev/null 2>/dev/null ; then
		if ! curl --version >/dev/null 2>/dev/null ; then
			echo "Please install wget or curl somewhere in your PATH"
			exit 1
		fi
		curl -o `basename $1` $1
		return $?
	else
		wget $1
		return $?
	fi
}

BOWTIE_BUILD_EXE=./bowtie2-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
	if ! which bowtie2-build ; then
		echo "Could not find bowtie2-build in current directory or in PATH"
		exit 1
	else
		BOWTIE_BUILD_EXE=`which bowtie2-build`
	fi
fi

INPUTS=
for c in $CHRS_TO_INDEX ; do
	if [ ! -f ${c}.fa ] ; then
		F=${c}.fa.gz
		get ${RN4_BASE}/$F || (echo "Error getting $F" && exit 1)
		gunzip $F || (echo "Error unzipping $F" && exit 1)
	fi
	[ -n "$INPUTS" ] && INPUTS=$INPUTS,${c}.fa
	[ -z "$INPUTS" ] && INPUTS=${c}.fa
done

CMD="${BOWTIE_BUILD_EXE} $* ${INPUTS} rn4"
echo Running $CMD
if $CMD ; then
	echo "rn4 index built; you may remove fasta files"
else
	echo "Index building failed; see error message"
fi
