kemal
368c97b9aa
- pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE, THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf) - CI workflow for Gitea/GitHub Actions: lint, type check, unit tests - fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36" bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug - make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs - plan §17: corrected P0 dataset table
80 lines
4.0 KiB
Bash
Executable File
80 lines
4.0 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Download SimurgArray datasets into data/<tier>/ and record sha256 checksums.
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# Vendor files are for personal research use only; never commit them.
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# Usage: bash scripts/fetch_data.sh p0|p1|p2
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set -euo pipefail
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cd "$(dirname "$0")/.."
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tier="${1:?usage: fetch_data.sh p0|p1|p2}"
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mkdir -p "data/$tier"
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sums="data/CHECKSUMS.sha256"; touch "$sums"
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get() { # get <url> <dest-dir>
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local url="$1" dir="$2" f
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f="$dir/$(basename "${url%%\?*}")"
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if [[ -s "$f" ]]; then echo "have $f"; else
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if command -v aria2c >/dev/null; then aria2c -x8 -s8 -c -d "$dir" "$url"
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else wget -c -P "$dir" "$url"; fi
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fi
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grep -q " $f\$" "$sums" || sha256sum "$f" >> "$sums"
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}
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unpack() { # unzip/untar every archive under <dir> next to itself (idempotent)
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find "$1" -name '*.zip' -o -name '*.tar.gz' | sort | while read -r a; do
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out="${a%.zip}"; out="${out%.tar.gz}"
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[[ -d "$out" ]] && continue
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mkdir -p "$out"
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case "$a" in *.zip) unzip -q -o "$a" -d "$out";; *.tar.gz) tar -xzf "$a" -C "$out";; esac
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done
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}
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GDA=https://webdata.illumina.com/downloads/productfiles/global-diversity-array
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G1K=https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip
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case "$tier" in
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p0)
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# GSA v4 PGx demo: 36 samples, real IDATs + BPM/CSV/EGT (primary small fixture)
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SUP=https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-gsa-pgx
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d=data/p0/gsa_v4_pgx; mkdir -p "$d"
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for f in idats_Demo_36.zip GSA-PGx-48v4-0_20079540_E2_bpm.zip GSA-PGx-48v4-0_20079540_E2_csv.zip \
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GSA-PGx-48v4-0_20079540_E2_ClusterFile.zip SampleSheetTemplate_GSAv4PGx_2beadchips.csv; do
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get "$SUP/$f" "$d"
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done
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# GDA v1 manifest/cluster files (note: the "Demo 36" bundle is a GenomeStudio project, not IDATs)
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d=data/p0/gda_v1; mkdir -p "$d"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm.zip" "$d"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-manifest-file-csv.zip" "$d"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-cluster-file.zip" "$d"
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get "https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/global-diversity-array/infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv" "$d"
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# Bioconductor IDAT fixtures (Artistic-2.0, redistributable) — fetched as source tarballs, no R needed
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d=data/p0/bioc; mkdir -p "$d"
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for pkg in IlluminaDataTestFiles hapmap370k; do
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url=$(curl -sL "https://bioconductor.org/packages/release/data/experiment/html/$pkg.html" \
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| grep -oE "\.\./src/contrib/${pkg}_[0-9.]+\.tar\.gz" | head -1 || true)
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[[ -n "$url" ]] && get "https://bioconductor.org/packages/release/data/experiment/${url#../}" "$d" \
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|| echo "!! could not resolve $pkg tarball"
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done
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unpack data/p0
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;;
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p1)
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d=data/p1/1kg_omni_broad; mkdir -p "$d"
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for f in HumanOmni2.5-4v1-Multi_B.bpm HumanOmni2.5-4v1_B.csv; do get "$G1K/broad_intensities/$f" "$d" || true; done
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echo "Listing broad_intensities/ (pick EGT + the 107 GB Omni25_idats_gtcs_2141_samples.tgz):"
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curl -s "$G1K/broad_intensities/" | grep -o 'href="[^"]*"' | cut -d'"' -f2 | grep -v '^?' || true
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echo "Then: bash scripts/fetch_data.sh p1-big (downloads the 107 GB archive)"
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d=data/p1/1kg_omni_sanger; mkdir -p "$d"
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echo "Sanger set index:"; curl -s "$G1K/sanger_intensities/" | grep -o 'href="[^"]*"' | cut -d'"' -f2 | grep -v '^?' || true
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d=data/p1/gse165845; mkdir -p "$d"
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get "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE165nnn/GSE165845/suppl/GSE165845_RAW.tar" "$d"
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;;
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p1-big)
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get "$G1K/broad_intensities/Omni25_idats_gtcs_2141_samples.tgz" data/p1/1kg_omni_broad
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;;
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p2)
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d=data/p2; mkdir -p "$d/gse96909" "$d/gda_pgx480"
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get "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96909/suppl/GSE96909_RAW.tar" "$d/gse96909"
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get "https://s3.amazonaws.com/webdata.illumina.com/downloads/productfiles/global-diversity-array-pgx/GDAPGx_Demo_idats.zip" "$d/gda_pgx480"
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;;
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*) echo "unknown tier $tier"; exit 2;;
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esac
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echo "checksums in $sums"
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