Version 2.4 (#67)

* kipoiseq version and use_strand * Bump version: 2.3.0 → 2.4.0 * cyvcf2 version * pyranges version
gagneurlab · May 23, 2023 · 31513da · 31513da
1 parent 3bef33d
commit 31513da
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diff --git a/mmsplice/__init__.py b/mmsplice/__init__.py
@@ -2,7 +2,7 @@
 
 __author__ = """Jun Cheng & M.Hasan Celik"""
 __email__ = 'chengju@in.tum.de'
-__version__ = '2.3.0'
+__version__ = '2.4.0'
 
 from tensorflow.keras.models import load_model
 from mmsplice.mmsplice import MMSplice, \

diff --git a/mmsplice/exon_dataloader.py b/mmsplice/exon_dataloader.py
@@ -235,7 +235,7 @@ def _next(self, exon, variant, overhang=None, mask_module=None):
         inputs = {
             'seq': self.fasta.extract(Interval(
                 exon.chrom, exon.start - overhang[0],
-                exon.end + overhang[1], strand=exon.strand)).upper(),
+                exon.end + overhang[1], strand=exon.strand), use_strand=True).upper(),
             'mut_seq': self.vseq_extractor.extract(
                 exon, [variant], overhang=overhang).upper()
         }

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.3.0
+current_version = 2.4.0
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -13,15 +13,16 @@
 
 requirements = [
     'setuptools',
-    'kipoiseq>=0.7,<0.8',
+    'kipoiseq',
     'cyvcf2',
     'tensorflow',
     'scipy',
     'pandas',
     'pyfaidx',
     'tqdm',
     'click',
-    'pyranges>=0.0.71'
+    'cyvcf2<=0.30.15',
+    'pyranges>=0.0.71,<0.0.126',
 ]
 
 setup_requirements = ['pytest-runner', ]
@@ -57,6 +58,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/gagneurlab/mmsplice',
-    version='2.3.0',
+    version='2.4.0',
     zip_safe=False
 )