Eric Coissac
c694e1f2b0
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
34 lines
1021 B
Bash
34 lines
1021 B
Bash
#!/usr/bin/env bash
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# Usage: simulate_one.sh genome.fna.gz output_dir
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# Simulates paired-end HiSeq reads for a single genome.
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set -euo pipefail
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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ISS="${SCRIPT_DIR}/../.venv/bin/iss"
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COVERAGE=15
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READ_LENGTH=150
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CPUS="${CPUS:-$(sysctl -n hw.logicalcpu 2>/dev/null || nproc 2>/dev/null || echo 2)}"
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genome_file="$1"
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out_dir="$2"
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mkdir -p "${out_dir}"
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tmp_fasta=$(mktemp "${TMPDIR:-/tmp}/obikmer_XXXXXX.fna")
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trap 'rm -f "${tmp_fasta}"' EXIT
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gzip -dc "${genome_file}" > "${tmp_fasta}"
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genome_size=$(grep -v "^>" "${tmp_fasta}" | tr -d '[:space:]' | wc -c | tr -d ' ')
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n_reads=$(python3 -c "import math; print(math.ceil(${COVERAGE} * ${genome_size} / (2 * ${READ_LENGTH})))")
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echo "[${out_dir}] genome=${genome_size} bp → ${n_reads} read pairs (${COVERAGE}x HiSeq)"
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"${ISS}" generate \
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--genomes "${tmp_fasta}" \
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--model HiSeq \
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--n_reads "${n_reads}" \
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--cpus "${CPUS}" \
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--compress \
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--output "${out_dir}/reads"
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