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1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
1 This file provides documentation for modules in Biopython that have been moved
2 or deprecated in favor of other modules. This provides some quick and easy
3 to find documentation about how to update your code to work again.
4
b4379ed @peterjc Dropping support for Python 2.3
peterjc authored
5 Python 2.3
6 ==========
7 No longer supported as of Release 1.51, having triggered a warning with
8 Release 1.50, with a mention in the release notes for Release 1.49.
9
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
10 Python 2.4
11 ==========
9cdfacb @peterjc Clarify Python 2.4 status in DEPRECATED file
peterjc authored
12 No longer supported as of Release 1.59, having triggered a warning since
13 Release 1.55, with advance notice in the release notes for Release 1.54.
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
14
3f17f75 @peterjc We are phasing out support for Python 2.5
peterjc authored
15 Python 2.5
16 ==========
17 Still supported, but has triggered a warning since Release 1.61.
18
e5ff9e4 @peterjc Talk about CompoundLocation and sub_features in DEPRECATED file
peterjc authored
19 Bio.SeqFeature
20 ==============
21 With the introduction of the CompoundLocation in Release 1.62, the SeqFeature
22 attribute sub_features was deprecated.
23
316c42a @peterjc Deprecate Bio.SeqIO.Interfaces class InterlacedSequenceIterator
peterjc authored
24 Bio.SeqIO.Interfaces
25 ====================
26 Unused class InterlacedSequenceIterator was deprecated in Release 1.61.
27
965dcf6 @semenko Deprecate Bio/HotRand.py
semenko authored
28 Bio.HotRand
29 ===========
30 Obsolete file Bio/HotRand.py was deprecated in Release 1.61, consider using
31 an alternative RNG, or the Python module "randomdotorg".
32
5a275cc @peterjc Formerly deprecate long obsolete file Bio/Search.py
peterjc authored
33 Bio.Search
34 ==========
35 Long obsolete file Bio/Search.py was deprecated in Release 1.61.
36
cbc7c87 @peterjc Deprecate Bio.Pathway.Rep.HashSet, use set instead.
peterjc authored
37 Bio.Pathway.Rep.HashSet
38 =======================
d678376 @peterjc Remove deprecated Bio.Pathway.Rep.HashSet
peterjc authored
39 Deprecated in Release 1.59, removed in Release 1.62. Use Python's built in
40 set object.
cbc7c87 @peterjc Deprecate Bio.Pathway.Rep.HashSet, use set instead.
peterjc authored
41
c52e986 @peterjc Make Bio.SeqFeature position objects act like and subclass int
peterjc authored
42 Bio.SeqFeature.WithinPosition and OneOfPosition
43 ===============================================
44 The arguments to create these fuzzy positions changed in Release 1.59.
45
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
46 Bio.Encodings
47 =============
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
48 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
49 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
50
51 Bio.PropertyManager
52 ===================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
53 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
54 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
55
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
56 Bio.InterPro
57 ============
4749068 @peterjc Remove deprecated Bio.InterPro module (HTML parser)
peterjc authored
58 This module was a parser for the EBI InterPro webpages, but no longer worked
59 with their current website. Deprecated in Release 1.55, and removed in
60 Release 1.58.
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
61
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
62 Bio.GenBank.LocationParser
63 ==========================
64 This module used to be used for parsing GenBank and EMBL feature locations.
65 It has been replaced with faster code using regular expressions, and is no
53d44f9 @peterjc Remove deprecated Bio.Parsers and Bio.GenBank.LocationParser
peterjc authored
66 longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56,
67 and removed in Release 1.59.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
68
69 Bio.Parsers and Bio.Parsers.spark
70 =================================
71 This module was a copy of John Aycock's SPARK parser included with Biopython
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
72 solely for use in Bio.GenBank.LocationParser. Declared obsolete in Release
53d44f9 @peterjc Remove deprecated Bio.Parsers and Bio.GenBank.LocationParser
peterjc authored
73 1.55, deprecated in Release 1.56, and removed in Release 1.59.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
74
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
75 Bio.Restriction.DNAUtils and check_bases
76 ========================================
77 This module (originally in C) offered complement and antiparallel functions
78 (duplicating functionality in Bio.Seq) and a rather odd function called
79 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
80 Deprecated in Release 1.53, removed in Release 1.57.
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
81
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
82 Bio.Blast.NCBIStandalone
83 ========================
84 The three functions for calling the "legacy" NCBI BLAST command line tools
85 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
86 1.53, and deprecated in Release 1.61. Please use the BLAST+ wrappers in
87 Bio.Blast.Applications instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
88
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
89 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
90 which was declared obsolete in Release 1.54. For some time now, both the NCBI
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
91 and Biopython have encouraged people to parse the XML output instead.
92
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
93 Bio.Blast.Applications
94 ======================
95 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
96 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
97 1.53 and deprecated in Release 1.61, having been replaced with wrappers for
98 the new NCBI BLAST+ tools (e.g. NcbiblastpCommandline and
99 NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
100
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
101 Bio.Clustalw
102 ============
9cbdf28 @peterjc Remove deprecated Bio.Clustalw module
peterjc authored
103 Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
104 removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
105 clustal format alignments (since Release 1.46), and Bio.Align.Applications
106 for calling the ClustalW command line tool (since Release 1.51). See the
107 Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
108
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
109 BioSQL and psycopg
110 ==================
111 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
3afd55b @peterjc Remove deprecated support for psycopg (v1) in BioSQL code
peterjc authored
112 in Release 1.51, and removed in Release 1.55. Please use psycopg2 instead.
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
113
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
114 Bio.Application.generic_run and ApplicationResult
115 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
116 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
117 Release 1.57. Please use the Python subprocess module instead, or as of
118 Release 1.55 the application wrappers can be used directly to execute the
119 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
120
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
121 Bio.Entrez.efetch and rettype="genbank"
122 =======================================
123 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
124 of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp"
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
125 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
126 automatically, but issues a deprecation warning. The code to check and correct
127 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
128
129 Bio.Entrez.query function
130 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
131 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
132
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
133 Bio.SwissProt.SProt
134 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
135 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
136 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
137 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
138
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
139 Bio.Prosite and Bio.Enzyme
140 ==========================
dcbdd45 @peterjc Removing deprecated Bio.Enzyme and Bio.Prosite modules
peterjc authored
141 Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in
142 Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and
04dcf21 @peterjc Minor correction to new module name
peterjc authored
143 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
144
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
145 Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredReader
146 ================================================
147 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredRe...
peterjc authored
148 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
149
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
150 Bio.File
151 ========
152 Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in
153 Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated
084c898 @peterjc Remove deprecated Bio.File.StringHandle and SGMLStripper
peterjc authored
154 in Release 1.57, removed in Release 1.61. Bio.File.StringHandle was deprecated
155 in Release 1.59, removed in Release 1.61.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
156
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
157 Bio.Graphics.GenomeDiagram and colour/color, centre/center
158 ==========================================================
159 GenomeDiagram originally used colour and centre (UK spelling of color and
160 center) for argument names. As part of its integration into Biopython 1.50,
161 this will support both colour and color, and both centre and center, to help
162 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
163 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
164 intend to eventually remove support for colour and centre in later releases
165 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
166
167 Bio.AlignAce and Bio.MEME
168 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been rem...
peterjc authored
169 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
170 in Release 1.56. Please use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
171
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
172 Numeric support
173 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
174 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
175 Please move to NumPy for Biopython 1.49 or later.
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
176
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
177 Bio.Seq and the data property
178 =============================
179 Direct use of the Seq object (and MutableSeq object) .data property is
e5fbcd7 Issue a DeprecatingWarning when accessing the .data property of Seq obje...
Michiel de Hoon authored
180 deprecated. As of Release 1.49, writing to the Seq object's .data property
181 triggered a warning, and this property was made read only in Release 1.53. In
182 Release 1.55 final, accessing the .data property gives a DeprecationWarning.
e3cf12a @peterjc Remove the deprecated Seq object's data property
peterjc authored
183 The Seq object's .data property was removed in Release 1.61.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warning w...
peterjc authored
184
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
185 Bio.Transcribe and Bio.Translate
186 ================================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
187 Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
188 in Release 1.57. Please use the methods or functions in Bio.Seq instead.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
189
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
190 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
191 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and st...
peterjc authored
192 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
193 deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53.
e7f44b5 @peterjc Updated DEPRECATED file now that Bio.mathfns and Bio.stringfns have been...
peterjc authored
194 The three C implementations were all removed in Release 1.53. Bio.mathfns
7a92530 @peterjc Removed deprecated Bio.listfns module
peterjc authored
195 and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in
196 Release 1.57.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
197
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
198 Bio.distance (and Bio.cdistance)
199 ================================
200 Bio.distance was deprecated in Release 1.49, at which point its C code
201 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
202 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
203
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
204 Bio.Ndb
205 =======
206 Deprecated in Release 1.49, as the website this parsed has been redesigned.
3972bd6 @peterjc Removing Bio.Ndb (deprecated a year ago in Biopython 1.49)
peterjc authored
207 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
208
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
209 Martel
210 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
211 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
212 in Release 1.51. The source code for Martel is still in our repository if
213 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
214
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
215 Bio.Mindy and associated modules.
216 =================================
217 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
218 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
219 Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.writ...
peterjc authored
220
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
221 Bio.Fasta index_file and Dictionary
222 ===================================
223 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
224 sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of
69f1dcc @peterjc Updated DEPRECATED file to reflect final name of Bio.SeqIO.index() funct...
peterjc authored
225 SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index()
8af957d @peterjc Adding the Bio.SeqIO.indexed_dict() function developed on a github branc...
peterjc authored
226 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
227
228 Bio.Fasta (including Bio.Fasta.FastaAlign)
229 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
230 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
231 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
232 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
233
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
234 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
235 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
236 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
237 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
238 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
239
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
240 Bio.Emboss.Primer
241 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Martel...
peterjc authored
242 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
243 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
244
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
245 Bio.Emboss.Applications
246 =======================
53f4841 @peterjc Remove deprecated EMBOSS PHYLIP wrappers
peterjc authored
247 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
248 obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in
249 release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g.
250 fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline,
251 EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
252 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
253 FConsenseCommandline, and FSeqBootCommandline, respectively.
254
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
255 Bio.MetaTool
256 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
257 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
258 for the output of MetaTool 3.5 which is now obsolete.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
259
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
260 Bio.GenBank
261 ===========
262 The online functionality (search_for, download_many, and NCBIDictionary) was
4f7d50c Removing the deprecated online bits of Bio.GenBank (replaced by Bio.Entr...
Peter Cock authored
263 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
264 in Release 1.54. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
265
266 Bio.PubMed
267 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
268 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
269 removed in Release 1.53. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
270
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
271 Bio.EUtils
272 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
273 Deprecated in favor of Bio.Entrez in Release 1.48, removed in Release 1.52.
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
274
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
275 Bio.Sequencing & Bio.Medline
276 ============================
277 A revised API was added and the old one deprecated in Release 1.48,
278 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
279 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
280 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
281 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
282 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
283 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
284 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
285
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
286 Bio.Blast.NCBIWWW
287 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
288 The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52.
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
289 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
290
291 Bio.Saf
292 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
293 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
294 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
295
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
296 Bio.NBRF
297 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
298 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
299 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
300
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
301 Bio.IntelliGenetics
302 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
303 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
304 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
305
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
306 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
307 =================================================================
308 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
309 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
310 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
311
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
312 Bio.SeqIO.to_alignment()
313 ========================
314 This function was made obsolete with the introduction of Bio.AlignIO,
9eb934e @peterjc Remove deprecated Bio.SeqIO.to_alignment function
peterjc authored
315 deprecated in Release 1.54, and removed in Release 1.58. Use either the
316 Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
317 directly instead.
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
318
5e507c9 Updating for release 1.47.
mdehoon authored
319 Bio.ECell
320 =========
321 Deprecated as of Release 1.47, as it appears to have no users, and the code
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
322 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
323
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
324 Bio.Ais
325 =======
326 Deprecated as of Release 1.45, removed in Release 1.49.
327
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
328 Bio.LocusLink
329 =============
330 Deprecated as of Release 1.45, removed in Release 1.49.
331 The NCBI's LocusLink was superseded by Entrez Gene.
332
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
333 Bio.SGMLExtractor
334 =================
335 Deprecated as of Release 1.46, removed in Release 1.49.
336
d01c450 Getting ready for release 1.46.
mdehoon authored
337 Bio.Rebase
338 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
339 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
340
341 Bio.Gobase
342 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
343 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
344
345 Bio.CDD
346 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
347 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
348
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
349 Bio.biblio
350 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
351 Deprecated as of Release 1.45, removed in Release 1.48
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
352
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
353 Bio.WWW
354 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
355 The modules under Bio.WWW were deprecated in Release 1.45, and removed in
2c7126b @peterjc Updating DEPRECATED file regarding Bio.Application and Bio.WWW
peterjc authored
356 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
357 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
358
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bio.W...
peterjc authored
359 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
360 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
361 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
362
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
363 Bio.SeqIO
364 =========
365 The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
366 the new Bio.SeqIO module as of Release 1.44, removed in Release 1.47.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
367
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
368 Bio.Medline.NLMMedlineXML
369 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
370 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
371
372 Bio.MultiProc
373 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
374 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
375
376 Bio.MarkupEditor
377 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
378 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
379
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
380 Bio.lcc
381 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
382 Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44, removed in 1.46.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
383
384 Bio.crc
385 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
386 Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44, removed in 1.46.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
387
388 Bio.FormatIO
389 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
390 This was removed in Release 1.44 (a deprecation was not possible).
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
391
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
392 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
393 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
394 These were deprecated in Release 1.44, and removed in Release 1.49.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
395
396 Bio.Kabat
397 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
398 This was deprecated in Release 1.43 and removed in Release 1.44.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
399
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
400 Bio.SeqUtils
401 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
402 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
403 in Release 1.31, and removed in Release 1.43. Function 'translate' was
404 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
405 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
406
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
407 Function makeTableX and classes ProteinX and MissingTable were deprecated
4804f1b @peterjc Remove deprecated makeTableX function and associated classes
peterjc authored
408 in Release 1.54, and removed in Release 1.58. These were remnants of the
409 removed translate function, and no longer served any useful purpose.
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
410
3178311 @peterjc Remove deprecated SeqUtils reverse function
peterjc authored
411 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
412 removed in Release 1.58. Instead just use the string's slice method with
413 a step of minus one.
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
414
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
415 Functions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
b6fd79e @peterjc Remove more deprecated functions in Bio.SeqUtils
peterjc authored
416 quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
417 in Release 1.58.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
418
3798b78 @peterjc Note quick_FASTA_reader -> SimpleFastaParser in DEPRECATED file
peterjc authored
419 Function quick_FASTA_reader was declared obsolete in Release 1.61. Use
420 function list(SimpleFastaParser(handle)) in Bio.SeqIO.FastaIO instead
421 (but ideally convert your code to using an iterator approach).
239b739 @peterjc Add a doctest to quick_FASTA_reader, declare it obsolete
peterjc authored
422
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
423 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
424 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
425 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
426 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
427 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
428
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
429 The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
430 in Release 1.57 (with the intention of reusing this name space for a GFF
431 parser).
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
432
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
433 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
434 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
435 Deprecated as of Release 1.30, removed in Release 1.42.
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
436 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
437
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
438 Bio.SVM
439 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
440 Deprecated as of Release 1.30, removed in Release 1.42.
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
441 The Support Vector Machine code in Biopython has been superseded by a
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
442 more robust (and maintained) SVM library, which includes a python
443 interface. We recommend using LIBSVM:
444
445 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
446
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
447 Bio.RecordFile
448 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
449 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
450 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
451
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
452 Bio.kMeans and Bio.xkMeans
453 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
454 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
455 the function kcluster in Bio.Cluster which performs k-means or k-medians
456 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
457
458 Bio.InterPro
459 ============
460 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
461 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
462
463 Bio.SCOP
464 ========
465 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
5af7ecc Removed Bio.SCOP.Dom.Iterator, which was deprecated
mdehoon authored
466 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
467 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
468
469 Bio.utils
470 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
471 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
472 and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
ca87378 @peterjc Adding a note to the Bio.utils section of the DEPRECATED file that this ...
peterjc authored
473 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
474 The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
475 Release 1.56, and removed in Release 1.57.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
476
477 Bio.Motif
478 =========
479 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
480 declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
481 in Release 1.57.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
482 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
483 in Release 1.53 and deprecated in Release 1.55 final; their functionality is
40ff78e Updating the DEPRECATED file concerning the parser simplifications in Bi...
mdehoon authored
484 now available through a read() function in Bio.Motif.Parsers.AlignAce.
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
485 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
486 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
487 deprecated in Release 1.55 final; their functionality is now available through
488 a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
489 respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace RecordPa...
mdehoon authored
490
491 Bio.Compass
492 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
493 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
c4d0fa8 @peterjc Remove deprecated bits of Bio.Compass
peterjc authored
494 deprecated in Release 1.55, removed in Release 1.59. Their functionality is
495 now available through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
496
497 Bio.Affy.CelFile
498 ================
499 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
9dfbc94 @peterjc Remove deprecated bits of Bio.Affy.CelFile
peterjc authored
500 in Release 1.54, deprecated in Release 1.55 and removed in Release 1.59.
501 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
502
503 Bio.PopGen.FDist
504 ================
505 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
3704a68 @peterjc Update NEWS and DEPRECATED files
peterjc authored
506 in Release 1.54, deprecated in Release 1.55, and removed in Release 1.58.
507 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
508
509 Bio.UniGene
510 ===========
511 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
512 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
513 Bio.UniGene were declared obsolete in Release 1.54, deprecated in Release 1.55,
ecdde52 @peterjc Correct typo in last commit
peterjc authored
514 and removed in Release 1.59. Their functionality is now available through a
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
515 read() and a parse() function in Bio.UniGene.
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
516 The HTML parser in Bio.UniGene.UniGene was declared obsolete in Release 1.59,
517 and deprecated in Release 1.61.
815d64f making the obsolete classes more explicit
mdehoon authored
518
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
519 Bio.SubsMat
520 ===========
521 The methods letter_sum and all_letters_sum were removed from the SeqMat class in
522 Bio.SubsMat in Release 1.57.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
523
524 Bio.Align
525 =========
526 The methods get_column and add_sequence of the MultipleSeqAlignment class were
527 deprecated in Release 1.57. The Alignment class in Bio.Align.Generic and its
528 method get_seq_by_num were deprecated in Release 1.57.
c13d64d Updating comments and DEPRECATED file
Michiel de Hoon authored
529
530 Bio.ParserSupport
531 =================
532 Bio.ParserSupport was declared obsolete in Release 1.59.
084c898 @peterjc Remove deprecated Bio.File.StringHandle and SGMLStripper
peterjc authored
533
534 Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59, and
535 removed in Release 1.61.
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