Eric Coissac
26026288de
Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
104 lines
3.1 KiB
Bash
Executable File
104 lines
3.1 KiB
Bash
Executable File
#!/usr/bin/env bash
|
|
# Usage: index_one_presence.sh SPECIMEN
|
|
# SPECIMEN = "species--strain" (Make pattern stem)
|
|
# Outputs:
|
|
# specimen_index_presence/SPECIMEN/index.done (written by obikmer)
|
|
# stats/indexing_presence/SPECIMEN.stats (one CSV data row, no header)
|
|
set -euo pipefail
|
|
|
|
SPECIMEN="$1"
|
|
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
|
|
RUN_DIR="${SCRIPT_DIR}/run"
|
|
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
|
|
|
|
species="${SPECIMEN%%--*}"
|
|
strain="${SPECIMEN#*--}"
|
|
|
|
READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
|
|
INDEX_PATH="${RUN_DIR}/specimen_index_presence/${SPECIMEN}"
|
|
STATS_DIR="${RUN_DIR}/stats/indexing_presence"
|
|
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
|
|
|
|
mkdir -p "${STATS_DIR}"
|
|
|
|
r1="${READS_DIR}/reads_R1.fastq.gz"
|
|
r2="${READS_DIR}/reads_R2.fastq.gz"
|
|
if [[ ! -f "${r1}" || ! -f "${r2}" ]]; then
|
|
echo "ERROR: reads not found in ${READS_DIR}" >&2
|
|
exit 1
|
|
fi
|
|
|
|
echo "[${SPECIMEN}] indexing (presence) → ${INDEX_PATH}"
|
|
|
|
STDERR_LOG=$(mktemp)
|
|
trap 'rm -f "${STDERR_LOG}"' EXIT
|
|
|
|
"${BINARY}" index \
|
|
--output "${INDEX_PATH}" \
|
|
--force \
|
|
--theta 0 \
|
|
--label "${SPECIMEN}" \
|
|
--meta "species=${species}" \
|
|
"${r1}" "${r2}" \
|
|
2>"${STDERR_LOG}"
|
|
|
|
cat "${STDERR_LOG}" >&2
|
|
|
|
python3 - "${species}" "${strain}" "${STDERR_LOG}" <<'PYEOF' >"${STATS_FILE}"
|
|
import sys, re
|
|
|
|
species, strain, logfile = sys.argv[1], sys.argv[2], sys.argv[3]
|
|
|
|
def strip_ansi(s):
|
|
return re.sub(r'\x1b\[[\x30-\x3f]*[\x20-\x2f]*[\x40-\x7e]', '', s)
|
|
|
|
def parse_wall(s):
|
|
s = s.strip()
|
|
if s.endswith('ms'): return float(s[:-2]) / 1000.0
|
|
if s.endswith('s'): return float(s[:-1])
|
|
return 0.0
|
|
|
|
def parse_rss(s):
|
|
m = re.match(r'([\d.]+)\s*(GB|MB|KB|B)', s.strip())
|
|
if not m: return 0
|
|
return int(float(m.group(1)) * {'GB': 1<<30, 'MB': 1<<20, 'KB': 1024, 'B': 1}[m.group(2)])
|
|
|
|
def is_sep(s):
|
|
return bool(s) and not re.search(r'[A-Za-z0-9]', s)
|
|
|
|
stats = {}
|
|
state = 'scan'
|
|
|
|
with open(logfile, errors='replace') as fh:
|
|
for raw in fh:
|
|
line = strip_ansi(raw.rstrip('\n'))
|
|
s = line.strip()
|
|
if state == 'scan':
|
|
if re.search(r'\bstage\b.*\bwall\b', line):
|
|
state = 'in_header'
|
|
elif state == 'in_header':
|
|
if is_sep(s): state = 'rows'
|
|
elif state == 'rows':
|
|
if is_sep(s): state = 'total'
|
|
elif s:
|
|
parts = re.split(r' +', s)
|
|
if len(parts) >= 4:
|
|
stats[parts[0]] = (parse_wall(parts[1]), parse_rss(parts[3]))
|
|
elif state == 'total':
|
|
if s:
|
|
parts = re.split(r' +', s)
|
|
if len(parts) >= 3:
|
|
stats[parts[0]] = (parse_wall(parts[1]),
|
|
parse_rss(parts[3]) if len(parts) > 3 else 0)
|
|
break
|
|
|
|
STAGE_ORDER = ['scatter', 'dereplicate', 'count_kmer', 'index']
|
|
row = [species, strain]
|
|
for stage in STAGE_ORDER:
|
|
w, r = stats.get(stage, ('', ''))
|
|
row += [f'{w:.3f}' if isinstance(w, float) else '', str(r)]
|
|
tw, tr = stats.get('TOTAL', ('', ''))
|
|
row += [f'{tw:.3f}' if isinstance(tw, float) else '', str(tr)]
|
|
print(','.join(row))
|
|
PYEOF
|