79 lines
2.3 KiB
Bash
79 lines
2.3 KiB
Bash
#!/bin/sh
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#
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# Downloads sequence for the GRCm37 release 81 version of M. Musculus (mouse) from
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# Ensembl.
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#
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# By default, this script builds and index for just the base files,
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# since alignments to those sequences are the most useful. To change
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# which 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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ENSEMBL_RELEASE=84
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ENSEMBL_GRCm38_BASE=ftp://ftp.ensembl.org/pub/release-${ENSEMBL_RELEASE}/fasta/mus_musculus/dna
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DBSNP_RELEASE=142
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SNP_FILE=snp${DBSNP_RELEASE}Common.txt
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UCSC_COMMON_SNP=http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/${SNP_FILE}
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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 $?
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fi
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}
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HISAT2_BUILD_EXE=./hisat2-build
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if [ ! -x "$HISAT2_BUILD_EXE" ] ; then
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if ! which hisat2-build ; then
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echo "Could not find hisat2-build in current directory or in PATH"
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exit 1
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else
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HISAT2_BUILD_EXE=`which hisat2-build`
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fi
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fi
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HISAT2_SNP_SCRIPT=./hisat2_extract_snps_haplotypes_UCSC.py
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if [ ! -x "$HISAT2_SNP_SCRIPT" ] ; then
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if ! which hisat2_extract_snps_haplotypes_UCSC.py ; then
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echo "Could not find hisat2_extract_snps_haplotypes_UCSC.py in current directory or in PATH"
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exit 1
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else
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HISAT2_SNP_SCRIPT=`which hisat2_extract_snps_haplotypes_UCSC.py`
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fi
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fi
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rm -f genome.fa
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F=Mus_musculus.GRCm38.dna.primary_assembly.fa
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if [ ! -f $F ] ; then
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get ${ENSEMBL_GRCm38_BASE}/$F.gz || (echo "Error getting $F" && exit 1)
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gunzip $F.gz || (echo "Error unzipping $F" && exit 1)
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mv $F genome.fa
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fi
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if [ ! -f $SNP_FILE ] ; then
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get ${UCSC_COMMON_SNP}.gz || (echo "Error getting ${UCSC_COMMON_SNP}" && exit 1)
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gunzip ${SNP_FILE}.gz || (echo "Error unzipping ${SNP_FILE}" && exit 1)
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awk 'BEGIN{OFS="\t"} {if($2 ~ /^chr/) {$2 = substr($2, 4)}; if($2 == "M") {$2 = "MT"} print}' ${SNP_FILE} > ${SNP_FILE}.tmp
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mv ${SNP_FILE}.tmp ${SNP_FILE}
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${HISAT2_SNP_SCRIPT} genome.fa ${SNP_FILE} genome
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fi
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CMD="${HISAT2_BUILD_EXE} -p 4 genome.fa --snp genome.snp --haplotype genome.haplotype genome_snp"
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echo Running $CMD
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if $CMD ; then
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echo "genome 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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