Peter Cock
Many of the Python files in Biopython still have self-tests at the end which are executed if the file is run directly via the idiom: ``` python if __name__ ==...
See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and ``__add__``, need to do the same specifically for integer offsets. Workaround ``feature + (-5)`` instead of ``feature - 5``, see https://twitter.com/tomeraltman/status/1473764959347638273
As part of #2046 we are moving from ``Seq`` objects having an alphabet object from ``Bio.Alphabets``, to recording the molecule type in the ``SeqRecord`` annotations instead. Currently this recycles the...
- [x] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [x] I have read the...
Python 3.9 adds these new string methods, which to me would apply equally well to sequence manipulation too - for example removing a start or stop codon, or prefixed barcode/adaptor...
Migrated from https://redmine.open-bio.org/issues/2034 which I filed in 2006-06-27. Cross reference #292 which added output in this format. > This is a slightly updated version of the code I posted to...
GitHub actions recently broke under Linux, e.g. ``` ====================================================================== ERROR: Bio.motifs.jaspar.db ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/MySQLdb/__init__.py", line 18, in from . import _mysql ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: cannot allocate...
I would need to go back over some (ideally merged) pull requests to check, but my strong impression compared to when we ran TravisCI/CircleCI/AppVeyor to now with GitHub Actions/CircleCI/AppVeyor, the...
Historically we used TravisCI for continous integration testing with multiple command line tools like NCBI BLAST+ and PAML installed via apt-get: https://github.com/biopython/biopython/blob/biopython-179/.travis.yml#L122 Currently we are only considering optional Python dependencies...
The docstrings for the PAML run methods seem a little confusing/out-of-date about the return values. https://github.com/biopython/biopython/blob/biopython-172/Bio/Phylo/PAML/_paml.py#L88 *"Return a process signal so the user can determine if the execution was successful...