Comments (4)
Mutant phage pinetree script and genbank file to replicate error:
phage_mutant_model.zip
from pinetree.
We decided the error seems to be something about having overlapping genes. It's true the documentation say that you can't use overlapping genes or even overlapping RBSs.
https://pinetree.readthedocs.io/en/latest/python_ref.html#pinetree.Genome.add_gene
However, for the T7 example, it successfully loads and runs a model that has overlapping genes?
https://github.com/clauswilke/pinetree/blob/master/examples/phage_model.py
This is a dump of the gene start-end that it is loading at this line to create the model
phage.add_gene(name=name, start=start, stop=stop, rbs_start=start - 30, rbs_stop=start, rbs_strength=1e7)
Several genes overlap, such as gene 5.9 and gene 6, gene 1.1 and gene 1.2, etc. unless I'm missing something?
gene 0.3 (positions 891 - 1468 )
protein_kinase-0.7 (positions 1469 - 3138 )
rnapol-1 (positions 3139 - 5887 )
gene 1.2 (positions 5888 - 6448 )
gene 1.1 (positions 6007 - 6135 )
gene 1.3 (positions 6449 - 7588 )
gene 1.4 (positions 7608 - 7763 )
gene 1.5 (positions 7791 - 7880 )
gene 1.6 (positions 7906 - 8166 )
gene 1.7 (positions 8166 - 8756 )
gene 1.8 (positions 8749 - 8895 )
gp-2 (positions 8898 - 9092 )
gene 2.5 (positions 9158 - 9856 )
gene 2.8 (positions 9857 - 10276 )
gene 3 (positions 10257 - 10706 )
lysozyme-3.5 (positions 10706 - 11161 )
gene 3.8 (positions 11225 - 11590 )
gene 4A (positions 11565 - 13265 )
gene 4.2 (positions 12988 - 13326 )
gene 4.3 (positions 13352 - 13564 )
gene 4.5 (positions 13584 - 13853 )
gene 4.7 (positions 13927 - 14334 )
gene 5 (positions 14353 - 16467 )
gene 5.3 (positions 16483 - 16839 )
gene 5.5 (positions 16851 - 17150 )
gene 5.7 (positions 17150 - 17359 )
gene 5.9 (positions 17359 - 17517 )
gene 6 (positions 17504 - 18406 )
gene 6.3 (positions 18394 - 18507 )
gene 6.5 (positions 18605 - 18859 )
gene 6.7 (positions 18864 - 19130 )
gene 7 (positions 19130 - 19531 )
gene 7.3 (positions 19535 - 19834 )
gene 7.7 (positions 19848 - 20240 )
gene 8 (positions 20240 - 21850 )
gene 9 (positions 21950 - 22873 )
gene 10A (positions 22967 - 24004 )
gene 11 (positions 24228 - 24818 )
gene 12 (positions 24842 - 27226 )
gene 13 (positions 27307 - 27723 )
gene 14 (positions 27728 - 28318 )
gene 15 (positions 28325 - 30568 )
gene 16 (positions 30595 - 34551 )
gene 17 (positions 34624 - 36285 )
gene 17.5 (positions 36344 - 36547 )
gene 18 (positions 36553 - 36822 )
gene 18.5 (positions 36917 - 37348 )
gene 18.7 (positions 37032 - 37283 )
gene 19 (positions 37370 - 39130 )
gene 19.2 (positions 38016 - 38273 )
gene 19.3 (positions 38553 - 38726 )
gene 19.5 (positions 39389 - 39538 )
from pinetree.
I suspect overlapping genes are necessary but not sufficient to cause the crash. I'd also argue that a crash is always bad. Pinetree should either accept the input genome and run without crash or reject the input genome as containing features that aren't supported. Since overlapping genes are common in bacteriophages, it would be best if we could identify the cause of the undefined behavior and fix it.
from pinetree.
I agree. I'm going to mark this as resolved, and then link it to a new issue that addresses this more generally.
from pinetree.
Related Issues (10)
- Lotka-Volterra test segfaults with sufficient time HOT 1
- Pinetree should be able to handle overlapping genes HOT 1
- Add a unit test so that we don't accidentally revert the race condition fix in polymer::move
- Support for multiple genomes HOT 1
- Codon usage / translation frames
- Update documentation to have copy_number instead of copies
- Unable to install pinetree HOT 6
- Travis setup is broken
- Read the Docs build is failing
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