More references

DoubleHelixApp · May 17, 2024 · 7ce91b4 · 7ce91b4
1 parent c5422a2
commit 7ce91b4
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Showing 2 changed files with 6 additions and 11 deletions.
diff --git a/wgse/metadata/references.json b/wgse/metadata/references.json
diff --git a/wgse/reference_genome/repository_manager.py b/wgse/reference_genome/repository_manager.py
@@ -143,17 +143,17 @@ def _create_companion_files(self, genome: Genome, force=False):
             _external.make_dictionary(genome.fasta, genome.dict)
         else:
             logging.info(f"{genome}: Dictionary file exists.")
-    
+
     def self_test(self):
         for index, reference in enumerate(self.genomes):
             if reference.sequences is None:
                 try:
                     logging.info(f"Processing {reference} as it has no sequences.")
-                    genome = manager.ingest(
+                    genome = self.ingest(
                         reference.fasta_url, reference.source, reference.build
                     )
-                    manager.genomes[index] = genome
-                    manager._loader.save(manager.genomes)
+                    self.genomes[index] = genome
+                    self._loader.save(self.genomes)
                 except Exception as e:
                     logging.critical(e)
 
@@ -191,9 +191,4 @@ def ingest(
         logging.info(f"4/4: Extracting sequence data: {compressor_output.name}.")
         self._create_companion_files(genome)
         genome.sequences = self._get_sequences(genome)
-        return genome
-
-
-if __name__ == "__main__":
-    manager = RepositoryManager()
-    manager.self_test()
+        return genome