diff --git a/charcoal/compare_taxonomy.py b/charcoal/compare_taxonomy.py index 47176cd..ee373e1 100644 --- a/charcoal/compare_taxonomy.py +++ b/charcoal/compare_taxonomy.py @@ -120,7 +120,6 @@ def choose_genome_lineage(guessed_genome_lineage, provided_lineage, match_rank, def get_genome_taxonomy(genome_name, genome_gather_json_filename, provided_lineage, tax_assign, match_rank, min_f_ident, min_f_major): - guessed_genome_lineage, f_major, f_ident = "", 0.0, 0.0 # did we get gather results? genome_info = utils.load_contigs_gather_json(genome_gather_json_filename) diff --git a/charcoal/gather_taxonomy.py b/charcoal/gather_taxonomy.py index e5ba93b..40f77e9 100644 --- a/charcoal/gather_taxonomy.py +++ b/charcoal/gather_taxonomy.py @@ -44,7 +44,7 @@ def main(args): new_siglist = [] for ss in siglist: if genome_sig.similarity(ss) == 1.0: - print(f'removing an identical match: {ss.name()}') + print(f'removing an identical match: {ss.name}') else: new_siglist.append(ss) siglist = new_siglist @@ -110,7 +110,7 @@ def main(args): # genome search genome_len=0 entire_mh = genome_sig.minhash - genome_name = os.path.basename(genome_sig.name()) + genome_name = os.path.basename(genome_sig.name) num_hashes = len(entire_mh.hashes) if not genome_len: for record in screed_iter: diff --git a/charcoal/just_taxonomy.py b/charcoal/just_taxonomy.py index afbf3f9..5087d40 100644 --- a/charcoal/just_taxonomy.py +++ b/charcoal/just_taxonomy.py @@ -386,10 +386,10 @@ def report(*args): new_siglist.append(ss) else: if args.lineage and args.lineage != 'NA': - report(f'found exact match: {ss.name()}. removing.') + report(f'found exact match: {ss.name}. removing.') identical_match_removed = True else: - report(f'found exact match: {ss.name()}. but no provided lineage! exiting.') + report(f'found exact match: {ss.name}. but no provided lineage! exiting.') comment = "Exact match in matches, but no provided lineage." create_empty_output(genomebase, comment, args.summary, None, args.contig_report, diff --git a/charcoal/utils.py b/charcoal/utils.py index 62cc233..e726084 100644 --- a/charcoal/utils.py +++ b/charcoal/utils.py @@ -180,7 +180,7 @@ def summarize_at_rank(lincounts, rank): def get_ident(sig): "Hack and slash identifiers." - ident = sig.name() + ident = sig.name ident = ident.split()[0] ident = ident.split('.')[0] return ident diff --git a/tests/test-data/loomba/contam.json b/tests/test-data/loomba/contam.json index daf58fe..578ca41 100644 --- a/tests/test-data/loomba/contam.json +++ b/tests/test-data/loomba/contam.json @@ -1 +1 @@ -[[[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes"]], 14], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Lachnospirales"]], 12], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Ruminococcaceae"]], 24], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Oscillospiraceae"]], 17], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], 1503]] \ No newline at end of file +{"loomba": [[[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Lachnospirales"], ["family", "f__Anaerotignaceae"], ["genus", "g__Anaerotignum"]], 7], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__An200"]], 3], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Oscillospiraceae"], ["genus", "g__Flavonifractor"]], 1], [[["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Acutalibacteraceae"], ["genus", "g__Anaeromassilibacillus"]], [["superkingdom", "d__Bacteria"], ["phylum", "p__Firmicutes_A"], ["class", "c__Clostridia"], ["order", "o__Oscillospirales"], ["family", "f__Oscillospiraceae"], ["genus", "g__Flavonifractor"]], 3]]} \ No newline at end of file diff --git a/tests/test_decontam.py b/tests/test_decontam.py index 585c37a..2f9c63b 100644 --- a/tests/test_decontam.py +++ b/tests/test_decontam.py @@ -70,7 +70,7 @@ def make_lca_and_lineages(match_files, lineages_csv, scaled, ksize, # build database of matches & lineages! for ss in siglist: - print(ss.name(), ss.minhash.scaled) + print(ss.name, ss.minhash.scaled) ident = just_taxonomy.get_ident(ss) lineage = tax_assign[ident]