Merge pull request #3 from malachig/master

update to work up to ensembl v105
genome · Apr 21, 2022 · f8b5982 · f8b5982
2 parents 90ae305 + d7c5ddf
commit f8b5982
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,4 +8,5 @@ test/data
 submit_to_pip.sh
 agfusion.egg-info/
 dist/
-*pyc
+*pyc
+*.swp
diff --git a/Dockerfile b/Dockerfile
@@ -19,7 +19,7 @@ RUN pip3 install mysqlclient
 
 # INSTALL AGFUSION & DATABASE FILES
 
-ENV ensembl_version=95
+ENV ensembl_version=105
 
 # Download latest AGFusion from source and install with pip
 WORKDIR /usr/local/bin

diff --git a/agfusion/utils.py b/agfusion/utils.py
@@ -15,7 +15,7 @@
 # this is mostly contigent on the maximum ensembl release supported
 # by pyensembl
 
-MAX_ENSEMBL_RELEASE = 95
+MAX_ENSEMBL_RELEASE = 105
 
 GENOME_SHORTCUTS = {
     'GRCm38':['mus_musculus',MAX_ENSEMBL_RELEASE],
@@ -61,8 +61,10 @@
 for i in range(67,MAX_ENSEMBL_RELEASE+1):
     if i < 68:
         ENSEMBL_MYSQL_TABLES['mus_musculus'][i] = 'mus_musculus_core_' + str(i) + '_37'
-    else:
+    elif i < 103:
         ENSEMBL_MYSQL_TABLES['mus_musculus'][i] = 'mus_musculus_core_' + str(i) + '_38'
+    else:
+        ENSEMBL_MYSQL_TABLES['mus_musculus'][i] = 'mus_musculus_core_' + str(i) + '_39'
 
 # min amino acid length of domain to plot it
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,4 +8,5 @@ test/data @@
     submit_to_pip.sh
     agfusion.egg-info/
     dist/
-    *pyc
+    *pyc
+    *.swp