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|
#!/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 indexes all these files. 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 $RANDOM_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
|
