41 lines
1.3 KiB
Bash
Executable File
41 lines
1.3 KiB
Bash
Executable File
#!/usr/bin/env bash
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# H1 genome-wide: run the per-chromosome H1 pipeline for all autosomes (chr1..22).
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# Idempotent — skips chroms already trained. Disables per-chrom figures by default
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# (set SKIP_FIGURES= to enable).
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#
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# Usage:
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# bash experiments/h1_representation/run_genome.sh
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# bash experiments/h1_representation/run_genome.sh chr2 chr5 # only these
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# SKIP_FIGURES= bash experiments/h1_representation/run_genome.sh # render figures
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set -euo pipefail
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REPO="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
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# Skip per-chrom UMAP/compare figures during genome loop (slow; render manually
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# for representative chroms after aggregation).
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export SKIP_FIGURES="${SKIP_FIGURES-1}"
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if [ $# -gt 0 ]; then
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CHROMS=("$@")
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else
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CHROMS=()
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for i in $(seq 1 22); do CHROMS+=("chr$i"); done
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fi
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START=$(date +%s)
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N=${#CHROMS[@]}
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i=0
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for CHROM in "${CHROMS[@]}"; do
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i=$((i + 1))
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echo ""
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echo "================================================================"
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echo "[H1] $CHROM ($i / $N)"
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echo "================================================================"
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CHROM="$CHROM" bash "$REPO/experiments/h1_representation/run.sh"
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done
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ELAPSED=$(( $(date +%s) - START ))
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echo ""
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echo "=== H1 genome-wide complete in ${ELAPSED}s ==="
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echo "Next: python experiments/h1_representation/aggregate.py"
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