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Remove deprecated Bio.SeqIO.to_alignment function

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1 parent a22b84c commit 9eb934ee0425b4636b26f310a0f1454f53745b17 @peterjc peterjc committed Aug 9, 2011
Showing with 3 additions and 26 deletions.
  1. +0 −24 Bio/SeqIO/__init__.py
  2. +3 −2 DEPRECATED
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@@ -861,30 +861,6 @@ def index_db(index_filename, filenames=None, format=None, alphabet=None,
return _index._SQLiteManySeqFilesDict(index_filename, filenames, format,
alphabet, key_function)
-def to_alignment(sequences, alphabet=None, strict=True):
- """Returns a multiple sequence alignment (DEPRECATED).
-
- - sequences -An iterator that returns SeqRecord objects,
- or simply a list of SeqRecord objects. All
- the record sequences must be the same length.
- - alphabet - Optional alphabet. Stongly recommended.
- - strict - Dummy argument, used to enable strict error
- checking of sequence lengths and alphabets.
- This is now always done.
-
- Using this function is now discouraged. You are now encouraged to use
- Bio.AlignIO instead, e.g.
-
- >>> from Bio import AlignIO
- >>> filename = "Clustalw/protein.aln"
- >>> alignment = AlignIO.read(filename, "clustal")
- """
- import warnings
- import Bio
- warnings.warn("The Bio.SeqIO.to_alignment(...) function is deprecated. "
- "Please use the Bio.Align.MultipleSeqAlignment(...) object "
- "directly instead.", Bio.BiopythonDeprecationWarning)
- return MultipleSeqAlignment(sequences, alphabet)
def convert(in_file, in_format, out_file, out_format, alphabet=None):
"""Convert between two sequence file formats, return number of records.
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@@ -283,8 +283,9 @@ old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
Bio.SeqIO.to_alignment()
========================
This function was made obsolete with the introduction of Bio.AlignIO,
-and deprecated in Release 1.54. Use either the Bio.AlignIO functions,
-or the Bio.Align.MultipleSeqAlignment class directly instead.
+deprecated in Release 1.54, and removed in Release 1.58. Use either the
+Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
+directly instead.
Bio.ECell
=========

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