refactor: make isRef calculation more specfic (#159)

galaxyproject · Nov 16, 2024 · 6e36129 · 6e36129
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commit 6e36129
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
@@ -47,7 +47,7 @@ def get_genome_row(genome_info):
     "taxon": genome_info["organism"]["organism_name"],
     "taxonomyId": genome_info["organism"]["tax_id"],
     "accession": genome_info["accession"],
-    "isRef": (not (refseq_category is None)) and ("reference" in refseq_category),
+    "isRef": refseq_category == "reference genome",
     "level": genome_info["assembly_info"]["assembly_level"],
     "chromosomeCount": genome_info["assembly_stats"].get("total_number_of_chromosomes"),
     "length": genome_info["assembly_stats"]["total_sequence_length"],

diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
@@ -3,7 +3,7 @@ Anopheles gambiae	7165	7
 Coccidioides immitis	5501	5
 Coccidioides posadasii	199306	13
 Culex pipiens	7175	5
-Mycobacterium tuberculosis	1773	7822
+Mycobacterium tuberculosis	1773	7823
 Plasmodium falciparum	5833	67
 Plasmodium vinckei	5860	10
 Plasmodium vivax	5855	19