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#!/bin/sh
#
# Downloads sequence for A. thaliana from TAIR and builds Bowtie index.
#
GENOMES_MIRROR=ftp://ftp.arabidopsis.org/home/tair
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 $?
fi
}
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie-build ; then
echo "Could not find bowtie-build in current directory or in PATH"
exit 1
else
BOWTIE_BUILD_EXE=`which bowtie-build`
fi
fi
FC=
for c in 1 2 3 4 5 C M ; do
if [ ! -f TAIR10_chr$c.fas ] ; then
FN=TAIR10_chr$c.fas
F=${GENOMES_MIRROR}/Sequences/whole_chromosomes/${FN}
[ -n "$FC" ] && FC="$FC,$FN"
[ -z "$FC" ] && FC=$FN
get $F || (echo "Error getting $F" && exit 1)
fi
if [ ! -f TAIR10_chr$c.fas ] ; then
echo "Could not find chr$c.fas file!"
exit 2
fi
done
CMD="${BOWTIE_BUILD_EXE} $* $FC a_thaliana"
echo $CMD
if $CMD ; then
echo "a_thaliana index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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