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 You're receiving this email because of your account on salsa.debian.org.
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