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#!/bin/sh
#
# Downloads sequence for the HG38 version of H. spiens (human) from
# UCSC.
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful. To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# variable below.
#
UCSC_HG38_BASE=http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips
F=hg38.chromFa.tar.gz
DBSNP_RELEASE=144
SNP_FILE=snp${DBSNP_RELEASE}Common.txt
UCSC_COMMON_SNP=http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/${SNP_FILE}
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --version >/dev/null 2>/dev/null ; then
echo "Please install wget or curl somewhere in your PATH"
exit 1
fi
curl -o `basename $1` $1
return $?
else
wget $1
return $?
fi
}
HISAT2_BUILD_EXE=./hisat2-build
if [ ! -x "$HISAT2_BUILD_EXE" ] ; then
if ! which hisat2-build ; then
echo "Could not find hisat2-build in current directory or in PATH"
exit 1
else
HISAT2_BUILD_EXE=`which hisat2-build`
fi
fi
HISAT2_SNP_SCRIPT=./hisat2_extract_snps_haplotypes_UCSC.py
if [ ! -x "$HISAT2_SNP_SCRIPT" ] ; then
if ! which hisat2_extract_snps.py ; then
echo "Could not find hisat2_extract_snps_haplotypes_UCSC.py in current directory or in PATH"
exit 1
else
HISAT2_SNP_SCRIPT=`which hisat2_extract_snps_haplotypes_UCSC.py`
fi
fi
rm -f genome.fa
get ${UCSC_HG38_BASE}/$F || (echo "Error getting $F" && exit 1)
tar xvzf $F || (echo "Error unzipping $F" && exit 1)
for i in {1..22}; do cat chroms/chr$i.fa >> genome.fa; done
cat chroms/chr[XYM].fa >> genome.fa
rm $F
if [ ! -f $SNP_FILE ] ; then
get ${UCSC_COMMON_SNP}.gz || (echo "Error getting ${UCSC_COMMON_SNP}" && exit 1)
${HISAT2_SNP_SCRIPT} genome.fa ${SNP_FILE}.gz genome
fi
CMD="${HISAT2_BUILD_EXE} -p 4 genome.fa --snp genome.snp --haplotype genome.haplotype genome"
echo Running $CMD
if $CMD ; then
echo "genome index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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