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|
#!/bin/sh
#
# Downloads sequence for the hg18 version of H. spiens (human) from
# UCSC.
#
# Note that UCSC's hg18 build has three categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
# 3. The alternative-haplotype files, named chr??_???_hap?.fa.gz
#
# By default, this script indexes files from categories 1 and 2. To
# change which categories are built by this script, edit the
# CHRS_TO_INDEX variable below.
#
BASE_CHRS="\
chr1 \
chr2 \
chr3 \
chr4 \
chr5 \
chr6 \
chr7 \
chr8 \
chr9 \
chr10 \
chr11 \
chr12 \
chr13 \
chr14 \
chr15 \
chr16 \
chr17 \
chr18 \
chr19 \
chr20 \
chr21 \
chr22 \
chrX \
chrY \
chrM"
RANDOM_CHRS="\
chr1_random \
chr2_random \
chr3_random \
chr4_random \
chr5_random \
chr6_random \
chr7_random \
chr8_random \
chr9_random \
chr10_random \
chr11_random \
chr13_random \
chr15_random \
chr16_random \
chr17_random \
chr18_random \
chr19_random \
chr21_random \
chr22_random \
chrX_random"
ALT_HAP_CHRS="\
chr22_h2_hap1 \
chr5_h2_hap1 \
chr6_cox_hap1 \
chr6_qbl_hap2"
CHRS_TO_INDEX="$BASE_CHRS $RANDOM_CHRS"
UCSC_HG18_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/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 ${UCSC_HG18_BASE}/$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} hg18"
echo Running $CMD
if $CMD ; then
echo "hg18 index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
|
