111 lines
3.4 KiB
Bash
111 lines
3.4 KiB
Bash
#!/bin/sh
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#
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# Downloads sequence for Zea mays AGPv3.31 from
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# Ensembl.
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#
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# The base files, named ??.fa.gz
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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=31
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ENSEMBL_DNA_BASE=ftp://ftp.ensemblgenomes.org/pub/plants/release-${ENSEMBL_RELEASE}/fasta/zea_mays/dna/
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ENSEMBL_GTF_BASE=ftp://ftp.ensemblgenomes.org/pub/plants/release-${ENSEMBL_RELEASE}/gtf/zea_mays/
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GTF_FILE=Zea_mays.AGPv3.31.gtf
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ENSEMBL_VCF_BASE=ftp://ftp.ensemblgenomes.org/pub/plants/release-${ENSEMBL_RELEASE}/vcf/zea_mays/
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VCF_FILE=zea_mays.vcf.gz
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ERCC_FILE=ERCC92
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ERCC_FTP=https://tools.thermofisher.com/content/sfs/manuals/${ERCC_FILE}.zip
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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_VCF_SCRIPT=./hisat2_extract_snps_haplotypes_VCF.py
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if [ ! -x "$HISAT2_VCF_SCRIPT" ] ; then
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if ! which hisat2_extract_snps_haplotypes_VCF.py ; then
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echo "Could not find hisat2_extract_snps_haplotypes_VCF.py in current directory or in PATH"
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exit 1
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else
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HISAT2_SNP_SCRIPT=`which hisat2_extract_snps_haplotypes_VCF.py`
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fi
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fi
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HISAT2_SS_SCRIPT=./hisat2_extract_splice_sites.py
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if [ ! -x "$HISAT2_SS_SCRIPT" ] ; then
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if ! which hisat2_extract_splice_sites.py ; then
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echo "Could not find hisat2_extract_splice_sites.py in current directory or in PATH"
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exit 1
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else
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HISAT2_SS_SCRIPT=`which hisat2_extract_splice_sites.py`
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fi
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fi
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HISAT2_EXON_SCRIPT=./hisat2_extract_exons.py
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if [ ! -x "$HISAT2_EXON_SCRIPT" ] ; then
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if ! which hisat2_extract_exons.py ; then
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echo "Could not find hisat2_extract_exons.py in current directory or in PATH"
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exit 1
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else
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HISAT2_EXON_SCRIPT=`which hisat2_extract_exons.py`
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fi
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fi
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rm -f genome.fa
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F=Zea_mays.AGPv3.31.dna.genome.fa
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if [ ! -f $F ] ; then
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get ${ENSEMBL_DNA_BASE}/$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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get ${ERCC_FTP} || (echo "Error getting ${ERCC_FILE}.zip" && exit 1)
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unzip ${ERCC_FILE}.zip
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cat ${ERCC_FILE}.fa >> genome.fa
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fi
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if [ ! -f $GTF_FILE ] ; then
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get ${ENSEMBL_GTF_BASE}/${GTF_FILE}.gz || (echo "Error getting ${GTF_FILE}" && exit 1)
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gunzip ${GTF_FILE}.gz || (echo "Error unzipping ${GTF_FILE}" && exit 1)
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cat ${ERCC_FILE}.gtf >> ${GTF_FILE}
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${HISAT2_SS_SCRIPT} ${GTF_FILE} > genome.ss
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${HISAT2_EXON_SCRIPT} ${GTF_FILE} > genome.exon
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fi
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if [ ! -f $VCF_FILE ] ; then
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get ${ENSEMBL_VCF_BASE}/${VCF_FILE} || (echo "Error getting ${ENSEMBL_VCF_BASE}/${VCF_FILE}" && exit 1)
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${HISAT2_VCF_SCRIPT} --non-rs genome.fa ${VCF_FILE} genome
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fi
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CMD="${HISAT2_BUILD_EXE} -p 4 genome.fa --snp genome.snp --haplotype genome.haplotype --ss genome.ss --exon genome.exon genome_snp_tran_ercc"
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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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