57 lines
1.2 KiB
Bash
57 lines
1.2 KiB
Bash
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#!/bin/sh
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#
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# Downloads sequence for A. thaliana from TAIR v10 and build Bowtie 2 index.
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#
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GENOMES_MIRROR=ftp://ftp.arabidopsis.org/home/tair
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get() {
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file=$1
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if ! wget --version >/dev/null 2>/dev/null ; then
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if ! curl --version >/dev/null 2>/dev/null ; then
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echo "Please install wget or curl somewhere in your PATH"
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exit 1
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fi
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curl -o `basename $1` $1
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return $?
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else
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wget $1
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return $?
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fi
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}
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BOWTIE_BUILD_EXE=./bowtie2-build
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if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
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if ! which bowtie2-build ; then
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echo "Could not find bowtie2-build in current directory or in PATH"
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exit 1
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else
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BOWTIE_BUILD_EXE=`which bowtie2-build`
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fi
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fi
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FC=
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for c in 1 2 3 4 5 C M ; do
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if [ ! -f TAIR10_chr$c.fas ] ; then
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FN=TAIR10_chr$c.fas
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F=${GENOMES_MIRROR}/Sequences/whole_chromosomes/${FN}
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[ -n "$FC" ] && FC="$FC,$FN"
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[ -z "$FC" ] && FC=$FN
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get $F || (echo "Error getting $F" && exit 1)
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fi
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if [ ! -f TAIR10_chr$c.fas ] ; then
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echo "Could not find chr$c.fas file!"
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exit 2
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fi
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done
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CMD="${BOWTIE_BUILD_EXE} $* $FC a_thaliana"
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echo $CMD
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if $CMD ; then
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echo "a_thaliana index built; you may remove fasta files"
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else
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echo "Index building failed; see error message"
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fi
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