31 lines
1.1 KiB
Plaintext
31 lines
1.1 KiB
Plaintext
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#!/bin/bash
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root=`dirname $0`
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url38="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz"
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url37d5="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
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if [ $# -eq 0 ]; then
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echo "Usage: $0 <hs38|hs38a|hs38d6|hs37|hs37d5>"
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exit 1;
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fi
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if [ $1 == "hs38d6" ]; then
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(wget -O- $url38 | gzip -dc; cat $root/resource-GRCh38/hs38d6-extra.fa) > $1.fa
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[ ! -f $1.fa.alt ] && cp $root/resource-GRCh38/hs38d6.fa.alt $1.fa.alt
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elif [ $1 == "hs38a" ]; then
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wget -O- $url38 | gzip -dc > $1.fa
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[ ! -f $1.fa.alt ] && grep _alt $root/resource-GRCh38/hs38d6.fa.alt > $1.fa.alt
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elif [ $1 == "hs38" ]; then
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wget -O- $url38 | gzip -dc | awk '/^>/{f=/_alt/?0:1}f' > $1.fa
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elif [ $1 == "hs37d5" ]; then
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wget -O- $url37d5 | gzip -dc > $1.fa 2>/dev/null
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elif [ $1 == "hs37" ]; then
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wget -O- $url37d5 | gzip -dc 2>/dev/null | awk '/^>/{f=/>hs37d5/?0:1}f' > $1.fa
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else
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echo "ERROR: unknown genome build"
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fi
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[ ! -f $1.fa.bwt ] && echo -e "\nPlease run 'bwa index $1.fa'...\n"
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