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.
119 lines
3.7 KiB
Python
119 lines
3.7 KiB
Python
#!/usr/bin/env python3
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"""Generate deps.mk — pure dependency declarations for the benchmark pipeline.
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Like C .d files: only target: prerequisites lines, no recipes.
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Recipes stay in the Makefile as generic rules.
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"""
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import gzip
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import re
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import sys
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from pathlib import Path
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STOP_WORDS = {'complete', 'chromosome', 'whole', 'sequence', 'genome',
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'endosymbiont', 'of'}
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STOP_PREFIXES = ('scaffold', 'contig', 'plasmid')
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def is_stop(tok):
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t = tok.lower()
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return t in STOP_WORDS or any(t.startswith(p) for p in STOP_PREFIXES)
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def sanitize(s):
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return re.sub(r'[^A-Za-z0-9._-]', '_', s).strip('_')
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def collect_tokens(text):
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parts = []
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for tok in text.split():
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tok = tok.rstrip(',.')
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if is_stop(tok):
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break
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parts.append(sanitize(tok))
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return '_'.join(filter(None, parts))
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def parse_organism(defn, gcf_id):
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words = defn.split()
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species = sanitize(words[0] + '_' + words[1])
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m = re.search(r'\bstr\.\s+(\S+)(?:\s+substr\.\s+(\S+))?', defn)
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if m:
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strain = sanitize(m.group(1))
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if m.group(2):
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strain += '_' + sanitize(m.group(2))
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return species, strain
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m = re.search(r'\bstrain\b\s+(.*)', defn)
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if m:
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strain = collect_tokens(m.group(1))
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if strain:
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return species, strain
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remainder = re.sub(r'^\S+ \S+\s*', '', defn)
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remainder = re.sub(r'^subsp\.\s+\S+\s*', '', remainder)
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remainder = re.sub(r'^serovar\s+\S+\s*', '', remainder)
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strain = collect_tokens(remainder)
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return species, strain if strain else gcf_id
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def first_definition(path):
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with gzip.open(path, 'rt') as fh:
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for line in fh:
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if line.startswith('>'):
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m = re.search(r'"definition":"([^"]*)"', line)
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return m.group(1) if m else line[1:].split()[0]
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return Path(path).stem
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def main():
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entries = [] # (specimen, species, sim_dir, genome_path)
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species_seen = []
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for path in sorted(sys.argv[1:]):
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gcf_id = Path(path).name.replace('_genomic.fna.gz', '')
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defn = first_definition(path)
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sp, st = parse_organism(defn, gcf_id)
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specimen = f'{sp}--{st}'
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sim_dir = f'simulated_data/{sp}/{st}'
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entries.append((specimen, sp, sim_dir, path))
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if sp not in species_seen:
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species_seen.append(sp)
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specimens = [e[0] for e in entries]
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print('SPECIMENS :=', ' '.join(specimens))
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print('SPECIES :=', ' '.join(species_seen))
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for specimen, species, sim_dir, genome in entries:
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reads = f'{sim_dir}/reads_R1.fastq.gz'
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p_done = f'specimen_index_presence/{specimen}/index.done'
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p_stats = f'stats/indexing_presence/{specimen}.stats'
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c_done = f'specimen_index_count/{specimen}/index.done'
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c_stats = f'stats/indexing_count/{specimen}.stats'
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ref = f'reference_index/{specimen}.npz'
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vp = f'stats/verify_presence/{specimen}.stats'
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vc = f'stats/verify_count/{specimen}.stats'
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print()
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print(f'# {specimen}')
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print(f'{reads}: {genome}')
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print(f'{ref}: {reads}')
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print(f'{p_done} {p_stats}: {reads}')
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print(f'{c_done} {c_stats}: {reads}')
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print(f'{vp}: {ref} {p_done}')
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print(f'{vc}: {ref} {c_done}')
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print()
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for sp in species_seen:
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sp_done = f'specific_index_presence/{sp}/index.done'
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sp_stats = f'stats/specific_kmer_presence/{sp}.stats'
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sc_done = f'specific_index_count/{sp}/index.done'
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sc_stats = f'stats/specific_kmer_count/{sp}.stats'
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print(f'# {sp}')
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print(f'{sp_done} {sp_stats}: global_index_presence/index.done')
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print(f'{sc_done} {sc_stats}: global_index_count/index.done')
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if __name__ == '__main__':
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main()
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