62 lines
1.3 KiB
Bash
62 lines
1.3 KiB
Bash
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#!/bin/sh
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#
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# Downloads sequence for the canFam2 version of C. familiaris (dog)
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# from UCSC.
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#
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i=2
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BASE_CHRS=chr1
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while [ $i -lt 39 ] ; do
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BASE_CHRS="$BASE_CHRS chr$i"
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i=`expr $i + 1`
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done
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BASE_CHRS="$BASE_CHRS chrX chrM chrUn"
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CHRS_TO_INDEX=$BASE_CHRS
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CANFAM2_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam2/chromosomes
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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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INPUTS=
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for c in $CHRS_TO_INDEX ; do
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if [ ! -f ${c}.fa ] ; then
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F=${c}.fa.gz
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get ${CANFAM2_BASE}/$F || (echo "Error getting $F" && exit 1)
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gunzip $F || (echo "Error unzipping $F" && exit 1)
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fi
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[ -n "$INPUTS" ] && INPUTS=$INPUTS,${c}.fa
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[ -z "$INPUTS" ] && INPUTS=${c}.fa
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done
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CMD="${BOWTIE_BUILD_EXE} $* ${INPUTS} canFam2"
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echo Running $CMD
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if $CMD ; then
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echo "canFam2 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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