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updating the DEPRECATED.rst file

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Michiel de Hoon
2025-09-18 15:28:14 +09:00
committed by Peter Cock
parent 5b2a50a9ce
commit 5a31cfce80
1 changed files with 10 additions and 9 deletions
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DEPRECATED.rst
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@ -108,8 +108,9 @@ NCBI said this API was no longer being maintained.
Bio.SCOP
--------
The ``search`` function was deprecated in Release 1.84. The CGI API this
wrapped is no longer available since SCOP moved to the EBI website.
The ``search`` function was deprecated in Release 1.84, and removed in Release
1.86. The CGI API this wrapped is no longer available since SCOP moved to the
EBI website.
Bio.AlignInfo
-------------
@ -186,8 +187,9 @@ hmmlearn (https://pypi.org/project/hmmlearn/) instead.
Bio.HMM
-------
The `Bio.HMM.DynamicProgramming`, `Bio.HMM.Trainer`, `Bio.HMM.MarkovModel`, and
`Bio.HMM.Utilities` modules were deprecated in release 1.82. Consider using
hmmlearn (https://pypi.org/project/hmmlearn/) instead.
`Bio.HMM.Utilities` modules were deprecated in release 1.82, and removed in
release 1.86. Consider using hmmlearn (https://pypi.org/project/hmmlearn/)
instead.
Bio.PDB.Polypeptide
-------------------
@ -229,8 +231,7 @@ deprecated in release 1.82, and removed in release 1.86. Instead of
``instances.search(sequence)``, ``sequence.search(instances)`` can be used,
where sequence is a Seq object. This allows instances to have different lengths.
The ``version`` parameter of the ``weblogo`` method of the ``Motif`` class in
``Bio.motifs`` was deprecated in release 1.83. Using the parameter has no
effect.
``Bio.motifs`` was deprecated in release 1.83, and removed in release 1.86.
The ``Instances`` class and the ``instances`` argument of the ``Motif`` class
initializer in ``Bio.motifs`` were deprecated in release 1.82, and removed in
@ -619,9 +620,9 @@ The Bio.SubsMat module was deprecated in Release 1.78, and removed in Release
Bio.Align
---------
The ``infer_coordinates`` class method of the ``Alignment`` class in
``Bio.Align`` was deprecated in Release 1.84. Instead,please use the
``parse_printed_alignment`` method, which is much faster, and returns both the
sequences after removing the gaps and the coordinates.
``Bio.Align`` was deprecated in Release 1.84, and removed in Release 1.86.
Instead, please use the ``parse_printed_alignment`` method, which is much
faster, and returns both the coordinates and sequences after removing the gaps.
The ``get_column`` method of the MultipleSeqAlignment was deprecated in
Release 1.57 and removed in Release 1.69.