[med-svn] [Git][med-team/pyensembl][master] 2 commits: New upstream version 2.1.0+ds

[Lance Lin (@linqigang)]

Lance Lin pushed to branch master at Debian Med / pyensembl


Commits:
a401f078 by Lance Lin at 2022-11-04T19:33:50+07:00
New upstream version 2.1.0+ds
- - - - -
2ce3ba36 by Lance Lin at 2022-11-04T19:33:50+07:00
Update upstream source from tag 'upstream/2.1.0+ds'

Update to upstream version '2.1.0+ds'
with Debian dir bdaf6fcaa3644c571319eebe28fa4ae1312ba39b
- - - - -


6 changed files:

- PKG-INFO
- pyensembl.egg-info/PKG-INFO
- pyensembl/ensembl_release_versions.py
- pyensembl/fasta.py
- pyensembl/transcript.py
- pyensembl/version.py


Changes:

=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyensembl
-Version: 2.0.1
+Version: 2.1.0
 Summary: Python interface to ensembl reference genome metadata
 Home-page: https://github.com/openvax/pyensembl
 Author: Alex Rubinsteyn


=====================================
pyensembl.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyensembl
-Version: 2.0.1
+Version: 2.1.0
 Summary: Python interface to ensembl reference genome metadata
 Home-page: https://github.com/openvax/pyensembl
 Author: Alex Rubinsteyn


=====================================
pyensembl/ensembl_release_versions.py
=====================================
@@ -11,7 +11,7 @@
 # limitations under the License.
 
 MIN_ENSEMBL_RELEASE = 54
-MAX_ENSEMBL_RELEASE = 107
+MAX_ENSEMBL_RELEASE = 108
 
 def check_release_number(release):
     """


=====================================
pyensembl/fasta.py
=====================================
@@ -51,9 +51,13 @@ def _parse_header_id(line):
     # .e.g.
     # "ENST00000448914.1" instead of "ENST00000448914"
     # So now we have to parse out the identifier
-    dot_index = identifier.find(b".")
-    if dot_index >= 0:
-        identifier = identifier[:dot_index]
+
+    # only split name of ENSEMBL naming. In other database, such as TAIR,
+    # the '.1' notation is the isoform not the version.
+    if identifier.startswith(b"ENS"):
+        dot_index = identifier.find(b".")
+        if dot_index >= 0:
+            identifier = identifier[:dot_index]
 
     return identifier.decode("ascii")
 


=====================================
pyensembl/transcript.py
=====================================
@@ -416,7 +416,10 @@ class Transcript(LocusWithGenome):
         Spliced cDNA sequence of transcript
         (includes 5" UTR, coding sequence, and 3" UTR)
         """
-        return self.genome.transcript_sequences.get(self.transcript_id.rsplit(".", 1)[0])
+        transcript_id = self.transcript_id
+        if transcript_id.startswith("ENS"):
+            transcript_id = transcript_id.rsplit(".", 1)[0]
+        return self.genome.transcript_sequences.get(transcript_id)
 
     @memoized_property
     def first_start_codon_spliced_offset(self):


=====================================
pyensembl/version.py
=====================================
@@ -1 +1 @@
-__version__ = '2.0.1'
+__version__ = '2.1.0'



View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/94dbd7acc4bd32039d3200190334c73b3f91e73d...2ce3ba36c9226c733a914fb31db10a400d59b83f

-- 
View it on GitLab: https://salsa.debian.org/med-team/pyensembl/-/compare/94dbd7acc4bd32039d3200190334c73b3f91e73d...2ce3ba36c9226c733a914fb31db10a400d59b83f
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