Update protein prefixes

mutalyzer · May 2, 2024 · bf7a0da · bf7a0da
1 parent caf96f2
commit bf7a0da
Showing 1 changed file with 11 additions and 3 deletions.
diff --git a/mutalyzer_retriever/sources/ncbi.py b/mutalyzer_retriever/sources/ncbi.py
@@ -191,10 +191,18 @@ def fetch(reference_id, reference_type, size_on=True, timeout=1):
     :returns tuple: raw annotations, type ("gff3" or "genbank")
     """
     db = "nuccore"
+    # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702849/
+    # https://support.nlm.nih.gov/knowledgebase/article/KA-03437/
+    # https://support.nlm.nih.gov/knowledgebase/article/KA-03434/
+    # https://support.nlm.nih.gov/knowledgebase/article/KA-03389/
+    # https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/
     if (
-        reference_id.startswith("NP")
-        or reference_id.startswith("XP")
-        or reference_id.startswith("WP")
+        reference_id.startswith("AP_")
+        or reference_id.startswith("NP_")
+        or reference_id.startswith("WP_")
+        or reference_id.startswith("XP_")
+        or reference_id.startswith("YP_")
+        or reference_id.startswith("ZP_")
     ):
         db = "protein"
     if reference_type in [None, "gff3"]: