* enable handling of <ligand> tags in UniProt XML files
* test parsing of <ligand> in UniProt XML
* add name to CONTRIB.rst
* format with black
* enable capture of multiple ligands from uniprot xml file. update tests accordingly
* add mock UniProt XML file with multiple ligand tags per feature
* test for correct len of all ligands list and multiple ligands per feature
Reverted unwanted changes (mostly arrays in tests, but also
some whitespace in doctests).
Remaining changes are standardising spacing between module
docstring and imports, and lower-case \x<hex> in strings.
* Add name to 'NEWS.rst' and 'CONTRIB.rst'
* Raise a warning when a SeqRecord is created using a string and also convert the argument to a Seq.
* Test that the BiopythonDeprecationWarning is raised when initializing a SeqRecord with a string.
Authored-by: Ernesto Rodriguez <ernesto.rodriguez@tum.de>
This fix uses the xml namespaces in the input to validate uniprot-xml
format in SeqIO, since the parser is already assuming the input has
uniprot namespace.
This will cause the parser to fail with a clear error message and prevent
misleading error messages like the OOM error in issue #4467
The test checks it aborts parsing when the input does not have the
expected xml namespace.
* Rename Bio.SeqFeature.FeatureLocation to SimpleLocation
Retain the old name as an alias for backward compatibility only.
* FeatureLocation -> SimpleLocation in DEPRECATED notes
* Avoid deprecated strand argument to SeqFeature
* Drop now redundant adjective simple in docstrings
Co-authored-by: Michiel de Hoon <mjldehoon@yahoo.com>
* move with block inside each submodule
* fix SeqXmlIO
* cleanup
* travis
* fix for python2
* travis being a jerk
* travis being a jerk
* hello goodbye
* putting changes back in
* travis being obnoxious
This reverts commit 3b46a068645fa8f98af5e7ddb7afdf699bf4e340
and the associated acknowledgements.
Sadly we don't (yet) have consent for the dual licensing, my
mistake in not catching this while reviewing the pull request.
raise 'Empty file.' error messages on encountering an empty file
instead of the current non standard errors. Formats affected are as
follows: cif-atom, pdb-atom, uniprot-xml.
This avoids a flake8-bugbear warning,
B008 Do not perform calls in argument defaults. The call is performed only once at function definition time. All calls to your function will reuse the result of that definition-time call. If this is intended, assign the function call to a module-level variable and use that variable as a default value.
We already have a module-level variable with a shared
instance of the generic protein alphabet - so use that.
Some mass spec location tags (`begin` and `end`) don't have `position` attributes. For example, one of them has `status="unknown". This causes a KeyError.`
