97 lines
1.9 KiB
Bash
97 lines
1.9 KiB
Bash
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#!/bin/sh
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#
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# Downloads sequence for the rn4 version of R. norvegicus (rat) from
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# UCSC.
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#
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# Note that UCSC's rn4 build has two categories of compressed fasta
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# files:
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#
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# 1. The base files, named chr??.fa.gz
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# 2. The unplaced-sequence files, named chr??_random.fa.gz
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#
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# By default, this script indexes all these files. To change which
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# categories are built by this script, edit the CHRS_TO_INDEX
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# variable below.
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#
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i=2
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BASE_CHRS=chr1
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while [ $i -lt 21 ] ; do
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BASE_CHRS="$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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RANDOM_CHRS="\
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chr1_random \
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chr2_random \
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chr3_random \
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chr4_random \
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chr5_random \
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chr6_random \
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chr7_random \
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chr8_random \
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chr9_random \
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chr10_random \
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chr11_random \
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chr12_random \
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chr13_random \
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chr14_random \
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chr15_random \
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chr16_random \
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chr17_random \
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chr18_random \
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chr19_random \
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chr20_random \
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chrX_random \
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chrUn_random"
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CHRS_TO_INDEX="$BASE_CHRS $RANDOM_CHRS"
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RN4_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/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 ${RN4_BASE}/$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} rn4"
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echo Running $CMD
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if $CMD ; then
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echo "rn4 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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