diff --git a/pyensembl/__init__.py b/pyensembl/__init__.py index d12d4ab..ca9645b 100644 --- a/pyensembl/__init__.py +++ b/pyensembl/__init__.py @@ -35,8 +35,7 @@ ) from .transcript import Transcript -__version__ = '0.8.14' - +__version__ = '0.9.0' _cache = {} diff --git a/pyensembl/biotypes.py b/pyensembl/biotypes.py index 3488f39..3c21c3f 100644 --- a/pyensembl/biotypes.py +++ b/pyensembl/biotypes.py @@ -217,13 +217,7 @@ 'non_stop_decay', # ordinary protein coding transcript 'protein_coding', - # usually a non-coding pseudogene but can be translated in some individuals - # depending on common genetic variation - 'polymorphic_pseudogene', - # Otherwise viable coding region omitted from this alternatively spliced - # transcript because the splice variation affects a region coding for a - # protein domain. - 'disrupted_domain', + # Gene in a "Locus Reference Genomic" region known to have disease-related # sequence variations. 'LRG_gene', @@ -237,9 +231,6 @@ coding_pseudogenes = { - # TODO: why is disrupted_domain a pseudogene rather than - # a translated protein we expect to be dysfunctional? - 'disrupted_domain', 'IG_C_pseudogene', 'IG_J_pseudogene', 'IG_pseudogene', @@ -263,6 +254,15 @@ 'translated_unprocessed_pseudogene', # pseudogene owing to a reverse transcribed and re-inserted sequence. "retrotransposed", + # usually a non-coding pseudogene but can be translated in some individuals + # depending on common genetic variation + 'polymorphic_pseudogene', + # Otherwise viable coding region omitted from this alternatively spliced + # transcript because the splice variation affects a region coding for a + # protein domain. + # TODO: why is disrupted_domain a pseudogene rather than + # a translated protein we expect to be dysfunctional? + 'disrupted_domain', } long_noncoding = {