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#!/bin/sh
#
# Downloads assembled sequence for M. musculus (mouse) from NCBI.
#
# From README_CURRENT_BUILD:
# Organism: Mus musculus (mouse)
# NCBI Build Number: 37
# Version: 1
# Release date: 05 July 2007
#
M_MUS_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/Assembled_chromosomes
M_MUS_MT_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/CHR_MT
OUTPUT=m_musculus_ncbi37
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=
append() {
[ -n "$INPUTS" ] && INPUTS=$INPUTS,$1
[ -z "$INPUTS" ] && INPUTS=$1
}
for c in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y ; do
F=mm_ref_chr$c.fa
if [ ! -f mm_ref_chr$c.fa ] ; then
FGZ=$F.gz
get $M_MUS_FTP/$FGZ || (echo "Error getting $FGZ" && exit 1)
gunzip $FGZ || (echo "Error unzipping $FGZ" && exit 1)
fi
append $F
done
F=mm_ref_chrMT.fa
if [ ! -f mm_ref_chrMT.fa ] ; then
FGZ=$F.gz
get $M_MUS_MT_FTP/$FGZ || (echo "Error getting $FGZ" && exit 1)
gunzip $FGZ || (echo "Error unzipping $FGZ" && exit 1)
fi
append $F
CMD="$BOWTIE_BUILD_EXE $* $INPUTS $OUTPUT"
echo $CMD
if $CMD ; then
echo "$OUTPUT index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
|
