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adding script to index latest human telomere-to-telomere genome provided at NCBI #418

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adding script to index latest human telomere-to-telomere genome provided at NCBI #418

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95e1f44
Script make_grch38.sh update to download sequence for the GRCh38 rele…
animesh Aug 2, 2023
4bb782a
adding script make_T2T_tran.sh to download sequence for the telomere-…
animesh Aug 5, 2023
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77 changes: 77 additions & 0 deletions scripts/make_T2T_tran.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,77 @@
#!/bin/sh

#
# Downloads sequence for the T2T-CHM13v2.0 of H. sapiens (human) from NCBI.
# ANNOTATION REPORT:
# https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/GCF_009914755.1-RS_2023_03
#

GENOME_RELEASE=GCF_009914755.1_T2T-CHM13v2.0_genomic
GENOME_BASE=https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/
GTF_FILE=$GENOME_RELEASE.gtf

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_SS_SCRIPT=./hisat2_extract_splice_sites.py
if [ ! -x "$HISAT2_SS_SCRIPT" ] ; then
if ! which hisat2_extract_splice_sites.py ; then
echo "Could not find hisat2_extract_splice_sites.py in current directory or in PATH"
exit 1
else
HISAT2_SS_SCRIPT=`which hisat2_extract_splice_sites.py`
fi
fi

HISAT2_EXON_SCRIPT=./hisat2_extract_exons.py
if [ ! -x "$HISAT2_EXON_SCRIPT" ] ; then
if ! which hisat2_extract_exons.py ; then
echo "Could not find hisat2_extract_exons.py in current directory or in PATH"
exit 1
else
HISAT2_EXON_SCRIPT=`which hisat2_extract_exons.py`
fi
fi

rm -f genome.fa
F=$GENOME_RELEASE.fna
if [ ! -f $F ] ; then
get ${GENOME_BASE}/$F.gz || (echo "Error getting $F" && exit 1)
gunzip $F.gz || (echo "Error unzipping $F" && exit 1)
else
cp $F genome.fa
fi


if [ ! -f $GTF_FILE ] ; then
get ${GENOME_BASE}/${GTF_FILE}.gz || (echo "Error getting ${GTF_FILE}" && exit 1)
gunzip ${GTF_FILE}.gz || (echo "Error unzipping ${GTF_FILE}" && exit 1)
else
${HISAT2_SS_SCRIPT} ${GTF_FILE} > genome.ss
${HISAT2_EXON_SCRIPT} ${GTF_FILE} > genome.exon
fi

${HISAT2_BUILD_EXE} -p 4 genome.fa --ss genome.ss --exon genome.exon genome_tran

2 changes: 1 addition & 1 deletion scripts/make_grch38_tran.sh
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Expand Up @@ -15,7 +15,7 @@
# variable below.
#

ENSEMBL_RELEASE=84
ENSEMBL_RELEASE=110
ENSEMBL_GRCh38_BASE=ftp://ftp.ensembl.org/pub/release-${ENSEMBL_RELEASE}/fasta/homo_sapiens/dna
ENSEMBL_GRCh38_GTF_BASE=ftp://ftp.ensembl.org/pub/release-${ENSEMBL_RELEASE}/gtf/homo_sapiens
GTF_FILE=Homo_sapiens.GRCh38.${ENSEMBL_RELEASE}.gtf
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