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clauswilke / pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates
http://pinetree.readthedocs.io
MIT License
11 stars 5 forks source link

Pinetree should be able to handle overlapping genes #12

Closed alexismhill3 closed 4 years ago

alexismhill3 commented 4 years ago

The documentation states that Pinetree doesn't support overlapping genes or genes that overlap with a ribosome binding site. Confusingly, if the user does try to add overlapping genes to the simulation, Pinetree will run anyway; this sometimes (but not always; see #11) results in a seemingly unrelated error.

Given that overlapping genes are quite abundant in real phage genomes, it would be best to fix this undefined behavior and implement full support for overlapping genes.

croots commented 4 years ago

This issue appears to occur in the example phage_model.py and the supplied wildtype genome if you use other randomness seeds, such as seed 45, with the default ignored genes.

RuntimeError: Polymerase __ribosome (start: 7762, stop: 7791, index: 9) is overlapping polymerase __ribosome (start: 7787, stop: 7816, index: 10) by more than one position on polymer __rna