Merge pull request #75 from Clinical-Genomics/fix_missing_exons

Use Ensembl v112 to temporarily address the missing exons issue
Clinical-Genomics · Dec 13, 2024 · 4dc2aa3 · 4dc2aa3
2 parents 8608a04 + 9a2fc2d
commit 4dc2aa3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 # [unreleased]
 ### Fixed
+- Some exons are missing when downloading build 38 data using Ensembl v.113 (Oct 2024). Using v.112 (May 2024) until the problem is fixed. Build 37 not affected.
+
+# [1.6.1]
+### Fixed
 - Security issue related to starlette version by updating fastapi, starlette and some dependencies
 - Updated urlib to v.2.2.3 to address the `urllib3's Proxy-Authorization request header isn't stripped during cross-origin redirects` issue
 - Updated certifi to v.2024.7.4 to address the `Certifi removes GLOBALTRUST root certificate` issue

diff --git a/schug/load/biomart.py b/schug/load/biomart.py
@@ -5,7 +5,7 @@
 
 LOG = logging.getLogger(__name__)
 BIOMART_37_URL = "https://feb2014.archive.ensembl.org/biomart/martservice?query="
-BIOMART_38_URL = "https://www.ensembl.org/biomart/martservice?query="
+BIOMART_38_URL = "https://may2024.archive.ensembl.org/biomart/martservice?query="
 
 
 class EnsemblXML: