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#!/bin/sh
#
# Downloads the sequence for a strain of e. coli from NCBI and builds a
# Bowtie index for it
#
GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
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
if [ ! -f NC_008253.fna ] ; then
if ! which wget > /dev/null ; then
echo wget not found, looking for curl...
if ! which curl > /dev/null ; then
echo curl not found either, aborting...
else
# Use curl
curl ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536_uid58531/NC_008253.fna -o NC_008253.fna
fi
else
# Use wget
wget ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536_uid58531/NC_008253.fna
fi
fi
if [ ! -f NC_008253.fna ] ; then
echo "Could not find NC_008253.fna file!"
exit 2
fi
CMD="${BOWTIE_BUILD_EXE} $* -t 8 NC_008253.fna e_coli"
echo $CMD
if $CMD ; then
echo "e_coli index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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