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Anticodons in bioperl are quoted when they line wrap, biopython does not. This inconsistency causes files output by biopython to fail to parse by some applications.
https://github.com/biopython/bio…
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Hi,
I am creating this issue to request support for incorporating BOLD database as a new module in Biopython. I see that there was a PR raised for the same purpose - https://github.com/biopython/bi…
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I have tried to find Biopython's changelog and couldn't find it. It took me quite some search to find `NEWS.rst` is what you call the changelog.
https://github.com/biopython/biopython/blob/master/N…
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Since Biopython 1.70 (commit a089000fcc64ef169286a5f26fce69de2639905d), ``setup.py`` has said via ``install_requires=...`` that numpy should be present (except on Jython which we used to support but d…
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NumPy 1.18.0 was released 22 December https://pypi.org/project/numpy/#history
https://numpy.org/devdocs/release/1.18.0-notes.html
At that point the master branch on TravisCI started failing, pypy3…
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**Are you using the latest release?**
Funannotate 1.8.15 with all dependencies installed properly (except optional genemark), as is stated in the tutorials and documentation
**Describe the bug**
…
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In the current rough ipynb the frame is picked manually, we want to do this automatically!
Possible useful tools people have already made:
- Manually find open reading frame: http://stackoverflow.com…
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In trying to run the EVcouplings pipeline, I couldn't download the MMTF files needed. Then I found the following message from RCSB:
"As of July 2, 2024, RCSB PDB will no longer serve PDB data in th…
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I ran pip install but it gave the following error:
```
Running setup.py bdist_wheel for biopython ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file_…
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When there are several different alignments with the best score, how does parasail choose which alignment/traceback to return? Can it enumerate all best-scoring alignments, in the manner of BioPython…