76 lines
2.0 KiB
Bash
76 lines
2.0 KiB
Bash
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#!/bin/sh
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#
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# Downloads sequence for the HG38 version of H. spiens (human) from
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# UCSC.
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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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UCSC_HG38_BASE=http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips
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F=hg38.chromFa.tar.gz
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DBSNP_RELEASE=144
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SNP_FILE=snp${DBSNP_RELEASE}Common.txt
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UCSC_COMMON_SNP=http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/${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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get ${UCSC_HG38_BASE}/$F || (echo "Error getting $F" && exit 1)
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tar xvzf $F || (echo "Error unzipping $F" && exit 1)
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for i in {1..22}; do cat chroms/chr$i.fa >> genome.fa; done
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cat chroms/chr[XYM].fa >> genome.fa
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rm $F
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if [ ! -f $SNP_FILE ] ; then
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get ${UCSC_COMMON_SNP}.gz || (echo "Error getting ${UCSC_COMMON_SNP}" && exit 1)
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${HISAT2_SNP_SCRIPT} genome.fa ${SNP_FILE}.gz genome
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fi
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CMD="${HISAT2_BUILD_EXE} -p 4 genome.fa --snp genome.snp --haplotype genome.haplotype genome"
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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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