118 lines
3.8 KiB
Bash
118 lines
3.8 KiB
Bash
#!/bin/sh
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#
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# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
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# Ensembl.
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#
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# Note that Ensembl's GRCh37 build has three categories of compressed fasta
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# files:
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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=75
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ENSEMBL_GRCh37_BASE=ftp://ftp.ensembl.org/pub/release-${ENSEMBL_RELEASE}/fasta/homo_sapiens/dna
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ENSEMBL_GRCh37_GTF_BASE=ftp://ftp.ensembl.org/pub/release-${ENSEMBL_RELEASE}/gtf/homo_sapiens
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GTF_FILE=Homo_sapiens.GRCh37.${ENSEMBL_RELEASE}.gtf
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DBSNP_RELEASE=144
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SNP_FILE=snp${DBSNP_RELEASE}Common.txt
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UCSC_COMMON_SNP=http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/${SNP_FILE}
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ERCC_FILE=ERCC92
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ERCC_FTP=https://tools.thermofisher.com/content/sfs/manuals/${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_SNP_SCRIPT=./hisat2_extract_snps_haplotypes_UCSC.py
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if [ ! -x "$HISAT2_SNP_SCRIPT" ] ; then
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if ! which hisat2_extract_snps_haplotypes_UCSC.py ; then
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echo "Could not find hisat2_extract_snps_haplotypes_UCSC.py in current directory or in PATH"
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exit 1
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else
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HISAT2_SNP_SCRIPT=`which hisat2_extract_snps_haplotypes_UCSC.py`
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fi
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fi
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HISAT2_SS_SCRIPT=./hisat2_extract_splice_sites.py
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if [ ! -x "$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 "$HISAT2_EXON_SCRIPT" ] ; then
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if ! which hisat2_extract_exons.py ; then
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echo "Could not find hisat2_extract_exons.py in current directory or in PATH"
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exit 1
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else
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HISAT2_EXON_SCRIPT=`which hisat2_extract_exons.py`
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fi
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fi
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rm -f genome.fa
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F=Homo_sapiens.GRCh37.${ENSEMBL_RELEASE}.dna.primary_assembly.fa
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if [ ! -f $F ] ; then
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get ${ENSEMBL_GRCh37_BASE}/$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 ${ENSEMBL_GRCh37_GTF_BASE}/${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 $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 --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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