add Junction class to models.py and related methods to other classes
add sqtl.py module to biosurfer/analysis, containing utility functions for analyzing sQTL effects on protein isoforms
add AnnotationFlag enum for easier categorization of pblocks (this is a rough prototype and will likely be superseded by a more complex Annotation class hierarchy)
add prototype sQTL analysis pipelines for specific datasets (tests/bone_sqtls.py and tests/copd_sqtls.py)
refactoring:
Gene.transcripts and Transcript.exons now use eager loading
initialization of some Transcript attributes moved out of object initialization and into cached_property (this is related to above change)
"demoted" many hybrid_property attributes to regular property since they are too complex to have corresponding SQLAlchemy expressions
main additions:
Junctionclass tomodels.pyand related methods to other classessqtl.pymodule tobiosurfer/analysis, containing utility functions for analyzing sQTL effects on protein isoformsAnnotationFlagenum for easier categorization of pblocks (this is a rough prototype and will likely be superseded by a more complex Annotation class hierarchy)tests/bone_sqtls.pyandtests/copd_sqtls.py)refactoring:
Gene.transcriptsandTranscript.exonsnow use eager loadingTranscriptattributes moved out of object initialization and intocached_property(this is related to above change)hybrid_propertyattributes to regularpropertysince they are too complex to have corresponding SQLAlchemy expressionscloses #66