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|
#!/bin/sh
#
# Downloads sequence for the mm9 version of M. musculus (mouse) from
# UCSC.
#
# Note that UCSC's mm9 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.
#
BASE_CHRS="\
chr1 \
chr2 \
chr3 \
chr4 \
chr5 \
chr6 \
chr7 \
chr8 \
chr9 \
chr10 \
chr11 \
chr12 \
chr13 \
chr14 \
chr15 \
chr16 \
chr17 \
chr18 \
chr19 \
chrX \
chrY \
chrM"
RANDOM_CHRS="\
1_random \
3_random \
4_random \
5_random \
7_random \
8_random \
9_random \
13_random \
16_random \
17_random \
X_random \
Y_random \
Un_random"
CHRS_TO_INDEX=$BASE_CHRS
UCSC_MM9_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/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 $?
fi
}
BOWTIE_BUILD_EXE=./bowtie-build
if [ ! -x "$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
INPUTS=
for c in $CHRS_TO_INDEX ; do
if [ ! -f ${c}.fa ] ; then
F=${c}.fa.gz
get ${UCSC_MM9_BASE}/$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} mm9"
echo Running $CMD
if $CMD ; then
echo "mm9 index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
|
