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.
103 lines
3.1 KiB
Bash
Executable File
103 lines
3.1 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Usage: index_one_presence.sh SPECIMEN
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# SPECIMEN = "species--strain" (Make pattern stem)
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# Outputs:
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# specimen_index_presence/SPECIMEN/index.done (written by obikmer)
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# stats/indexing_presence/SPECIMEN.stats (one CSV data row, no header)
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set -euo pipefail
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SPECIMEN="$1"
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SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
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BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
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species="${SPECIMEN%%--*}"
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strain="${SPECIMEN#*--}"
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READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
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INDEX_PATH="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}"
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STATS_DIR="${SCRIPT_DIR}/stats/indexing_presence"
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STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
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mkdir -p "${STATS_DIR}"
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r1="${READS_DIR}/reads_R1.fastq.gz"
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r2="${READS_DIR}/reads_R2.fastq.gz"
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if [[ ! -f "${r1}" || ! -f "${r2}" ]]; then
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echo "ERROR: reads not found in ${READS_DIR}" >&2
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exit 1
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fi
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echo "[${SPECIMEN}] indexing (presence) → ${INDEX_PATH}"
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STDERR_LOG=$(mktemp)
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trap 'rm -f "${STDERR_LOG}"' EXIT
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"${BINARY}" index \
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--output "${INDEX_PATH}" \
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--force \
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--theta 0 \
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--label "${SPECIMEN}" \
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--meta "species=${species}" \
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"${r1}" "${r2}" \
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2>"${STDERR_LOG}"
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cat "${STDERR_LOG}" >&2
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python3 - "${species}" "${strain}" "${STDERR_LOG}" <<'PYEOF' >"${STATS_FILE}"
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import sys, re
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species, strain, logfile = sys.argv[1], sys.argv[2], sys.argv[3]
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def strip_ansi(s):
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return re.sub(r'\x1b\[[\x30-\x3f]*[\x20-\x2f]*[\x40-\x7e]', '', s)
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def parse_wall(s):
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s = s.strip()
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if s.endswith('ms'): return float(s[:-2]) / 1000.0
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if s.endswith('s'): return float(s[:-1])
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return 0.0
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def parse_rss(s):
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m = re.match(r'([\d.]+)\s*(GB|MB|KB|B)', s.strip())
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if not m: return 0
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return int(float(m.group(1)) * {'GB': 1<<30, 'MB': 1<<20, 'KB': 1024, 'B': 1}[m.group(2)])
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def is_sep(s):
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return bool(s) and not re.search(r'[A-Za-z0-9]', s)
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stats = {}
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state = 'scan'
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with open(logfile, errors='replace') as fh:
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for raw in fh:
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line = strip_ansi(raw.rstrip('\n'))
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s = line.strip()
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if state == 'scan':
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if re.search(r'\bstage\b.*\bwall\b', line):
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state = 'in_header'
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elif state == 'in_header':
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if is_sep(s): state = 'rows'
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elif state == 'rows':
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if is_sep(s): state = 'total'
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elif s:
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parts = re.split(r' +', s)
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if len(parts) >= 4:
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stats[parts[0]] = (parse_wall(parts[1]), parse_rss(parts[3]))
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elif state == 'total':
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if s:
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parts = re.split(r' +', s)
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if len(parts) >= 3:
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stats[parts[0]] = (parse_wall(parts[1]),
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parse_rss(parts[3]) if len(parts) > 3 else 0)
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break
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STAGE_ORDER = ['scatter', 'dereplicate', 'count_kmer', 'index']
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row = [species, strain]
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for stage in STAGE_ORDER:
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w, r = stats.get(stage, ('', ''))
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row += [f'{w:.3f}' if isinstance(w, float) else '', str(r)]
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tw, tr = stats.get('TOTAL', ('', ''))
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row += [f'{tw:.3f}' if isinstance(tw, float) else '', str(tr)]
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print(','.join(row))
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PYEOF
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