test: Adjust for smafa 0.8.0.

wwood · May 29, 2024 · 5f79901 · 5f79901
1 parent 547e113
commit 5f79901
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Showing 10 changed files with 4 additions and 4 deletions.
diff --git a/test/data/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/test/data/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
diff --git a/test/data/22seqs.sdb/otus.sqlite3 b/test/data/22seqs.sdb/otus.sqlite3
diff --git a/...s.gpkg.spkg.smpkg/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/...s.gpkg.spkg.smpkg/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/otus.sqlite3 b/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/otus.sqlite3
diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json b/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json
@@ -1 +1 @@
-{"singlem_metapackage_version": 4, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null}
+{"singlem_metapackage_version": 5, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null, "taxonomy_database_name": "custom_taxonomy_database", "taxonomy_database_version": null, "diamond_prefilter_performance_parameters": "--block-size 0.5 --target-indexed -c1", "diamond_taxonomy_assignment_performance_parameters": "--block-size 0.5 --target-indexed -c1", "makeidx_sensitivity_params": null}
diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/prefilter.fna.dmnd b/test/data/4.11.22seqs.gpkg.spkg.smpkg/prefilter.fna.dmnd
diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/read_taxonomies.sqlite3 b/test/data/4.11.22seqs.gpkg.spkg.smpkg/read_taxonomies.sqlite3
diff --git a/...nual.json.v5.smafa_naive.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/...nual.json.v5.smafa_naive.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
diff --git a/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/otus.sqlite3 b/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/otus.sqlite3
diff --git a/test/test_pipe.py b/test/test_pipe.py
@@ -1112,7 +1112,7 @@ def test_smafa_naive_then_diamond_assignment_paired(self):
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),
@@ -1126,7 +1126,7 @@ def test_smafa_naive_then_diamond_assignment_paired_only_read2_hits(self):
             os.path.join(path_to_data, 'random.fna'), # i.e. no hits
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),
@@ -1140,7 +1140,7 @@ def test_smafa_naive_then_diamond_assignment_paired_only_read1_hits(self):
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, 'random.fna'), # i.e. no hits
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"singlem_metapackage_version": 4, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null}
		{"singlem_metapackage_version": 5, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null, "taxonomy_database_name": "custom_taxonomy_database", "taxonomy_database_version": null, "diamond_prefilter_performance_parameters": "--block-size 0.5 --target-indexed -c1", "diamond_taxonomy_assignment_performance_parameters": "--block-size 0.5 --target-indexed -c1", "makeidx_sensitivity_params": null}