Decide how to handle (or not) duplicate exon entries

standage / tag

Genome annotation data analysis and management implemented in pure Python

http://tag.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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Decide how to handle (or not) duplicate exon entries #30

Open standage opened 7 years ago

standage commented 7 years ago

For example, in case of alternative splicing, exons shared between isoforms can either be 1) duplicated or 2) have multiple Parent values.

standage commented 7 years ago

If we handle this, it should be a generator that consumes and yields entries of all types, but handles exon features (maybe arbitrary features?) correctly.

standage commented 7 years ago

For each feature CC create two dictionaries:

feature by ID
exon by range (defaultdict with range objects as keys and lists of exon entries as values)

For duplicated exons (lists with length > 1), add all parent IDs and add as child to appropriate parents.