Merge branch 'development'

docs/source/conf.py

@@ -20,13 +20,13 @@
 # -- Project information -----------------------------------------------------
 
 project = u'SplAdder'
-copyright = u'2019, Andre Kahles'
+copyright = u'2013-2022, Andre Kahles'
 author = u'Andre Kahles'
 
 # The short X.Y version
 version = u'3.0'
 # The full version, including alpha/beta/rc tags
-release = u'3.0.0'
+release = u'3.0.1'
 
 
 # -- General configuration ---------------------------------------------------

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.0.1
 commit = True
 tag = True
 

setup.py

@@ -45,6 +45,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/ratschlab/spladder',
-    version='3.0.0',
+    version='3.0.1',
     zip_safe=False,
 )

spladder/__init__.py

@@ -4,4 +4,4 @@
 
 __author__ = """Andre Kahles"""
 __email__ = '[email protected]'
-__version__ = '3.0.0'
+__version__ = '3.0.1'

spladder/alt_splice/events.py

@@ -142,13 +142,19 @@ def curate_alt_prime(event_list, options):
             elif event_list[i].exons1[1, 1] < event_list[i].exons2[1, 1]:
                 event_list[i].exons2[1, 1] = event_list[i].exons1[1, 1]
                 corr_count += 1
+            ### check whether our isoform convention is still met - if not, correct
+            if np.sum(event_list[i].exons1[:, 1] - event_list[i].exons1[:, 0]) > np.sum(event_list[i].exons2[:, 1] - event_list[i].exons2[:, 0]):
+                event_list[i].exons1, event_list[i].exons2 = event_list[i].exons2, event_list[i].exons1
         elif np.all(event_list[i].exons1[1, :] == event_list[i].exons2[1, :]):
             if event_list[i].exons1[0, 0] > event_list[i].exons2[0, 0]:
                 event_list[i].exons2[0, 0] = event_list[i].exons1[0, 0]
                 corr_count += 1
             elif event_list[i].exons1[0, 0] < event_list[i].exons2[0, 0]:
                 event_list[i].exons1[0, 0] = event_list[i].exons2[0, 0]
                 corr_count += 1
+            ### check whether our isoform convention is still met - if not, correct
+            if np.sum(event_list[i].exons1[:, 1] - event_list[i].exons1[:, 0]) > np.sum(event_list[i].exons2[:, 1] - event_list[i].exons2[:, 0]):
+                event_list[i].exons1, event_list[i].exons2 = event_list[i].exons2, event_list[i].exons1
 
     ### remove events with non-overlapping alt_exons
     if len(rm_idx) > 0: