From 5a31cfce801218e8a878d85baafb3402b144dc15 Mon Sep 17 00:00:00 2001 From: Michiel de Hoon Date: Thu, 18 Sep 2025 15:28:14 +0900 Subject: [PATCH] updating the DEPRECATED.rst file --- DEPRECATED.rst | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/DEPRECATED.rst b/DEPRECATED.rst index f0e47ac11..84552a460 100644 --- a/DEPRECATED.rst +++ b/DEPRECATED.rst @@ -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.