This is very much a sketch of an idea and will probably not be addressed in the initial release.
Common pattern among Biosurfer classes:
parent object with "interval" characteristics
children objects that are "subsets" of parent
may be of heterogeneous type (e.g. exons and ORFs are both children of a transcript)
user wants to know:
what children does a given parent have?
what is the parent of a given child?
for a defined relationship, which of the parent's other children are related to a given child?
most common relationship: overlapping coordinates
Would be nice to have some abstract data structure that implements all the above behavior in a robust way so that future development can be simpler / less redundant
Should provide similar behavior as SQLAlchemy's "relationship" objects but without depending on an underlying database (probably needs to work alongside SQLAlchemy relationships, though)
This is very much a sketch of an idea and will probably not be addressed in the initial release.
Common pattern among Biosurfer classes:
Would be nice to have some abstract data structure that implements all the above behavior in a robust way so that future development can be simpler / less redundant
Should provide similar behavior as SQLAlchemy's "relationship" objects but without depending on an underlying database (probably needs to work alongside SQLAlchemy relationships, though)