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tasks/genome-comparison/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 22: Pairwise Bacterial Genome Comparison
+#
+# DAG (depth 5):
+#
+# L0: genome_A.fna, genome_B.fna
+# L1: ├── prokka A          prokka B
+#     └── nucmer (whole-genome alignment A vs B)
+# L2: ├── dnadiff (alignment summary)
+#     │     └── show-snps (SNP extraction)
+#     └── panaroo (ortholog clustering from prokka GFFs)
+# L3: ├── SNP annotation (bedtools intersect SNPs with genes)
+#     └── unique gene extraction per genome
+# L4: MERGE
+# =============================================================================
+
+THREADS=$(( $(nproc) > 8 ? 8 : $(nproc) ))
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+DATA="${SCRIPT_DIR}/data"
+OUT="${SCRIPT_DIR}/outputs"
+RES="${SCRIPT_DIR}/results"
+
+GENOME_A="${DATA}/genome_A.fna"
+GENOME_B="${DATA}/genome_B.fna"
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}"/{prokka_A,prokka_B,nucmer,panaroo,snp_annotation} "${RES}"
+
+# ===========================================================================
+# L1-A: Annotate genome A
+# ===========================================================================
+log_step "L1-A: Prokka genome A"
+if [ ! -f "${OUT}/prokka_A/genome_A.gff" ]; then
+    prokka "${GENOME_A}" --outdir "${OUT}/prokka_A" --prefix genome_A \
+           --cpus ${THREADS} --kingdom Bacteria --force
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L1-B: Annotate genome B
+# ===========================================================================
+log_step "L1-B: Prokka genome B"
+if [ ! -f "${OUT}/prokka_B/genome_B.gff" ]; then
+    prokka "${GENOME_B}" --outdir "${OUT}/prokka_B" --prefix genome_B \
+           --cpus ${THREADS} --kingdom Bacteria --force
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L1-C: Whole-genome alignment with nucmer
+# ===========================================================================
+log_step "L1-C: nucmer alignment"
+if [ ! -f "${OUT}/nucmer/alignment.delta" ]; then
+    nucmer --prefix="${OUT}/nucmer/alignment" "${GENOME_A}" "${GENOME_B}"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L2-A: dnadiff summary statistics
+# ===========================================================================
+log_step "L2-A: dnadiff"
+if [ ! -f "${OUT}/nucmer/dnadiff.report" ]; then
+    dnadiff -d "${OUT}/nucmer/alignment.delta" -p "${OUT}/nucmer/dnadiff"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L2-B: Extract SNPs
+# ===========================================================================
+log_step "L2-B: show-snps"
+if [ ! -f "${OUT}/nucmer/snps.tsv" ]; then
+    show-snps -Clr "${OUT}/nucmer/alignment.delta" > "${OUT}/nucmer/snps.tsv"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L2-C: Panaroo ortholog comparison
+# ===========================================================================
+log_step "L2-C: Panaroo ortholog comparison"
+if [ ! -f "${OUT}/panaroo/summary_statistics.txt" ]; then
+    panaroo -i "${OUT}/prokka_A/genome_A.gff" "${OUT}/prokka_B/genome_B.gff" \
+            -o "${OUT}/panaroo" --clean-mode strict -c 0.98 \
+            --threads ${THREADS} 2>&1 || true
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L3: Parse results
+# ===========================================================================
+log_step "L3: Parse results"
+
+# dnadiff stats
+ALIGNED_BASES=$(grep "AlignedBases" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}' | sed 's/(.*//')
+AVG_IDENTITY=$(grep "AvgIdentity" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+TOTAL_SNPS=$(grep "TotalSNPs" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+TOTAL_INDELS=$(grep "TotalIndels" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+BREAKPOINTS=$(grep "Breakpoints" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+RELOCATIONS=$(grep "Relocations" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+INVERSIONS=$(grep "Inversions" "${OUT}/nucmer/dnadiff.report" | head -1 | awk '{print $2}')
+
+# Genome sizes
+LEN_A=$(awk '/^>/{if(l)s+=l; l=0; next}{l+=length}END{s+=l; print s}' "${GENOME_A}")
+LEN_B=$(awk '/^>/{if(l)s+=l; l=0; next}{l+=length}END{s+=l; print s}' "${GENOME_B}")
+
+# Gene counts from prokka
+CDS_A=$(grep "^CDS" "${OUT}/prokka_A/genome_A.txt" | awk '{print $2}')
+CDS_B=$(grep "^CDS" "${OUT}/prokka_B/genome_B.txt" | awk '{print $2}')
+
+# Panaroo: shared vs unique genes
+CORE=$(grep "Core genes" "${OUT}/panaroo/summary_statistics.txt" 2>/dev/null | awk '{print $NF}' || echo "0")
+TOTAL_PAN=$(grep "Total genes" "${OUT}/panaroo/summary_statistics.txt" 2>/dev/null | awk '{print $NF}' || echo "0")
+UNIQUE=$((TOTAL_PAN - CORE))
+
+# ===========================================================================
+# L4: MERGE
+# ===========================================================================
+log_step "L4-MERGE"
+
+cat > "${RES}/genome_comparison.csv" << CSVEOF
+metric,value
+genome_a_length,${LEN_A}
+genome_b_length,${LEN_B}
+aligned_bases,${ALIGNED_BASES}
+average_identity,${AVG_IDENTITY}
+total_snps,${TOTAL_SNPS}
+total_indels,${TOTAL_INDELS}
+breakpoints,${BREAKPOINTS}
+relocations,${RELOCATIONS}
+inversions,${INVERSIONS}
+cds_genome_a,${CDS_A}
+cds_genome_b,${CDS_B}
+shared_orthologs,${CORE}
+unique_genes,${UNIQUE}
+total_pangenome,${TOTAL_PAN}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/genome_comparison.csv"
+echo ""
+ls -lh "${RES}/"