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1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
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 ==========
12 As of Biopython 1.54, we consider support for Python 2.4 to be deprecated.
13 This means we will continue to support Python 2.4 for at least two further
14 releases, and at least one year (whichever takes longer), before dropping
15 support for Python 2.4. This can be delayed given feedback from our users
16 (e.g. if this proves to be a problem in combination with other libraries).
affab35 @peterjc Adding explicit warning to setup.py that support for Python 2.4 is be…
peterjc authored
17 An explicit warning was added to setup.py for Biopython 1.55.
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
18
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
19 Bio.Encodings
20 =============
28a7dae @peterjc Deprecate Bio.utils, Bio.PropertyManager and Bio.Encodings (see maili…
peterjc authored
21 Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
22
23 Bio.PropertyManager
24 ===================
28a7dae @peterjc Deprecate Bio.utils, Bio.PropertyManager and Bio.Encodings (see maili…
peterjc authored
25 Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
26
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI I…
peterjc authored
27 Bio.InterPro
28 ============
29 This module was a parser for the EBI InterPro webpages, but no longer works
30 with their current website. Deprecated in Release 1.55.
31
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
32 Bio.GenBank.LocationParser
33 ==========================
34 This module used to be used for parsing GenBank and EMBL feature locations.
35 It has been replaced with faster code using regular expressions, and is no
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.s…
peterjc authored
36 longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
37
38 Bio.Parsers and Bio.Parsers.spark
39 =================================
40 This module was a copy of John Aycock's SPARK parser included with Biopython
f38249a @peterjc Fixed a typo
peterjc authored
41 soley for use in Bio.GenBank.LocationParser. Declared obsolete in Release
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.s…
peterjc authored
42 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
43
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
44 Bio.Restriction.DNAUtils and check_bases
45 ========================================
46 This module (originally in C) offered complement and antiparallel functions
47 (duplicating functionality in Bio.Seq) and a rather odd function called
48 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
49 Deprecated in Release 1.53, removed in Release 1.57.
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
50
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
51 Bio.Blast.NCBIStandalone
52 ========================
53 The three functions for calling the "legacy" NCBI BLAST command line tools
54 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ad5ea06 @peterjc Clarify DEPRECATED file regarding application wrappers
peterjc authored
55 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
56
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
57 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
58 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 mailin…
peterjc authored
59 and Biopython have encouraged people to parse the XML output instead.
60
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
61 Bio.Blast.Applications
62 ======================
63 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
64 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
65 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
66 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as o…
peterjc authored
67
cbb051b @peterjc Note about the old EMBOSS PHYLIP wrappers being obsolete
peterjc authored
68 Bio.EMBOSS.Applications
69 =======================
70 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
71 obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
72 PHYLIP tools (e.g. fneighbor) instead.
73
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
74 Bio.Clustalw
75 ============
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
76 Declared obsolete in Release 1.52, and deprecated in Release 1.55 final,
77 having been replaced with Bio.AlignIO for parsing and writing clustal format
78 alignments (since Release 1.46), and Bio.Align.Applications for calling the
79 ClustalW command line tool (Release 1.51). See the Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
80
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
81 BioSQL and psycopg
82 ==================
83 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
84 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
85
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
86 Bio.Application.generic_run and ApplicationResult
87 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
88 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
89 Release 1.57. Please use the Python subprocess module instead, or as of
90 Release 1.55 the application wrappers can be used directly to execute the
91 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
92
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
93 Bio.Entrez.efetch and rettype="genbank"
94 =======================================
95 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
96 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
97 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
98 automatically, but issues a deprecation warning. The code to check and correct
99 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
100
101 Bio.Entrez.query function
102 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
103 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
104
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
105 Bio.SwissProt.SProt
106 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
107 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
108 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
109 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
110
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
111 Bio.Prosite and Bio.Enzyme
112 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
113 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
114 Most of the functionality has moved to Bio.ExPASy.Prosite and
115 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
116
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
117 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
118 =====================================================================
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.Filtere…
peterjc authored
119 Declared obsolete in Release 1.50, deprecated in Release 1.52, removed in
120 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
121
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
122 Bio.Graphics.GenomeDiagram and colour/color, centre/center
123 ==========================================================
124 GenomeDiagram originally used colour and centre (UK spelling of color and
125 center) for argument names. As part of its integration into Biopython 1.50,
126 this will support both colour and color, and both centre and center, to help
127 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
128 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
129 intend to eventually remove support for colour and centre in later releases
130 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
131
132 Bio.AlignAce and Bio.MEME
133 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been …
peterjc authored
134 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
135 in Release 1.56. Please use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
136
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
137 Numeric support
138 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
139 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
140 Please move to NumPy for Biopython 1.49 or later.
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
141
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
142 Bio.Seq and the data property
143 =============================
144 Direct use of the Seq object (and MutableSeq object) .data property is
e5fbcd7 Issue a DeprecatingWarning when accessing the .data property of Seq o…
Michiel de Hoon authored
145 deprecated. As of Release 1.49, writing to the Seq object's .data property
146 triggered a warning, and this property was made read only in Release 1.53. In
147 Release 1.55 final, accessing the .data property gives a DeprecationWarning.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warnin…
peterjc authored
148
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
149 Bio.Transcribe and Bio.Translate
150 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
151 Declared obsolete in Release 1.49, deprecated in Release 1.51.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
152 Please use the methods or functions in Bio.Seq instead.
153
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
154 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
155 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and…
peterjc authored
156 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
157 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 b…
peterjc authored
158 The three C implementations were all removed in Release 1.53. Bio.mathfns
159 and Bio.stringfns were removed in Release 1.55.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
160
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
161 Bio.distance (and Bio.cdistance)
162 ================================
163 Bio.distance was deprecated in Release 1.49, at which point its C code
164 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
165 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
166
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
167 Bio.Ndb
168 =======
169 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
170 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
171
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
172 Martel
173 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
174 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
175 in Release 1.51. The source code for Martel is still in our repository if
176 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
177
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
178 Bio.Mindy and associated modules.
179 =================================
180 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
181 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
182 Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.w…
peterjc authored
183
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
184 Bio.Fasta index_file and Dictionary
185 ===================================
186 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
187 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() fu…
peterjc authored
188 SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index()
8af957d @peterjc Adding the Bio.SeqIO.indexed_dict() function developed on a github br…
peterjc authored
189 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
190
191 Bio.Fasta (including Bio.Fasta.FastaAlign)
192 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
193 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
194 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
195 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
196
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
197 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
198 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
199 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
200 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
201 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
202
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
203 Bio.Emboss.Primer
204 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
205 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
206 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
207
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
208 Bio.Emboss.Applications
209 =======================
210 EProtDistCommandline, ENeighborCommandline, EProtParsCommandline,
211 EConsenseCommandline, and ESeqBootCommandline were declared obsolete in
212 Release 1.52, and deprecated in Release 1.55 final. These functions were
213 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
214 FConsenseCommandline, and FSeqBootCommandline, respectively.
215
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
216 Bio.MetaTool
217 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
218 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
219 for the output of MetaTool 3.5 which is now obsolete.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
220
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
221 Bio.GenBank
222 ===========
223 The online functionality (search_for, download_many, and NCBIDictionary) was
4f7d50c Removing the deprecated online bits of Bio.GenBank (replaced by Bio.E…
Peter Cock authored
224 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
225 in Release 1.54. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
226
227 Bio.PubMed
228 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
229 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
230 removed in Release 1.53. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
231
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
232 Bio.EUtils
233 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
234 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
235
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
236 Bio.Sequencing & Bio.Medline
237 ============================
238 A revised API was added and the old one deprecated in Release 1.48,
239 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
240 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
241 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
242 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
243 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
244 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
245 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
246
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
247 Bio.Blast.NCBIWWW
248 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
249 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…
peterjc authored
250 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
251
252 Bio.Saf
253 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
254 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
255 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
256
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
257 Bio.NBRF
258 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
259 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
260 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
261
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
262 Bio.IntelliGenetics
263 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
264 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
265 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
266
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
267 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
268 =================================================================
269 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
270 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
271 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
272
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
273 Bio.SeqIO.to_alignment()
274 ========================
275 This function was made obsolete with the introduction of Bio.AlignIO,
276 and deprecated in Release 1.54. Use either the Bio.AlignIO functions,
277 or the Bio.Align.MultipleSeqAlignment class directly instead.
278
5e507c9 Updating for release 1.47.
mdehoon authored
279 Bio.ECell
280 =========
281 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…
peterjc authored
282 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
283
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
284 Bio.Ais
285 =======
286 Deprecated as of Release 1.45, removed in Release 1.49.
287
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
288 Bio.LocusLink
289 =============
290 Deprecated as of Release 1.45, removed in Release 1.49.
291 The NCBI's LocusLink was superseded by Entrez Gene.
292
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
293 Bio.SGMLExtractor
294 =================
295 Deprecated as of Release 1.46, removed in Release 1.49.
296
d01c450 Getting ready for release 1.46.
mdehoon authored
297 Bio.Rebase
298 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
299 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
300
301 Bio.Gobase
302 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
303 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
304
305 Bio.CDD
306 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
307 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
308
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
309 Bio.biblio
310 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
311 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 t…
peterjc authored
312
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
313 Bio.WWW
314 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
315 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
316 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
317 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
318
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bi…
peterjc authored
319 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
320 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
321 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
322
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
323 Bio.SeqIO
324 =========
325 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…
peterjc authored
326 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
327
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
328 Bio.Medline.NLMMedlineXML
329 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
330 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
331
332 Bio.MultiProc
333 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
334 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
335
336 Bio.MarkupEditor
337 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
338 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
339
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
340 Bio.lcc
341 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
342 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
343
344 Bio.crc
345 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
346 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
347
348 Bio.FormatIO
349 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
350 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
351
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
352 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
353 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
354 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
355
356 Bio.Kabat
357 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
358 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
359
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
360 Bio.SeqUtils
361 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
362 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
363 in Release 1.31, and removed in Release 1.43. Function 'translate' was
364 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
365 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
366
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
367 Function makeTableX and classes ProteinX and MissingTable were deprecated
368 in Release 1.54. These were remnants of the removed translate function,
369 and no longer served any useful purpose.
370
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
371 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
372 just use the string's slice method with a step of minus one.
373
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
374 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
375 quicker_apply_on_multi_fasta were deprecated in Release 1.55 final.
376
377
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
378 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
379 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
380 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
381 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
382 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
383
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
384 The whole of the old Bio.GFF module was deprecated in Release 1.53
385 (with the intention of reusing this name space for a GFF parser).
386
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
387 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
388 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
389 Deprecated as of Release 1.30, removed in Release 1.42.
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
390 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
391
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
392 Bio.SVM
393 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
394 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
395 The Support Vector Machine code in Biopython has been superceeded by a
396 more robust (and maintained) SVM library, which includes a python
397 interface. We recommend using LIBSVM:
398
399 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
400
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
401 Bio.RecordFile
402 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
403 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
404 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
405
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
406 Bio.kMeans and Bio.xkMeans
407 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
408 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
409 the function kcluster in Bio.Cluster which performs k-means or k-medians
410 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
411
412 Bio.InterPro
413 ============
414 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
415 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
416
417 Bio.SCOP
418 ========
419 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
420 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
421 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
422
423 Bio.utils
424 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
425 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
426 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 th…
peterjc authored
427 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
28a7dae @peterjc Deprecate Bio.utils, Bio.PropertyManager and Bio.Encodings (see maili…
peterjc authored
428 The whole of Bio.utils was declared obsolete in Release 1.55, and deprecated
429 in Biopython 1.56.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
430
431 Bio.Motif
432 =========
433 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
434 declared obsolete in Release 1.53, and deprecated in Release 1.55 final.
435 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
436 in Release 1.53 and deprecated in Release 1.55 final; their functionality is
40ff78e Updating the DEPRECATED file concerning the parser simplifications in…
mdehoon authored
437 now available through a read() function in Bio.Motif.Parsers.AlignAce.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
438 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser, _MASTScanner,
439 and MASTRecord were declared obsolete in Release 1.54 and deprecated in Release
440 1.55 final; their functionality is now available through a read() function in
815d64f making the obsolete classes more explicit
mdehoon authored
441 Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST, respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace Record…
mdehoon authored
442
443 Bio.Compass
444 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
445 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
446 and deprecated in Release 1.55 final. Their functionality is now available
447 through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
448
449 Bio.Affy.CelFile
450 ================
451 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
452 in Release 1.54. Their functionality is now available through a read()
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
453 function. These classes were deprecated in Release 1.55 final.
815d64f making the obsolete classes more explicit
mdehoon authored
454
455 Bio.PopGen.FDist
456 ================
457 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
f70cc43 Adding DeprecationWarnings to obsolete code in Bio.PopGen.FDist. Appl…
Michiel de Hoon authored
458 in Release 1.54, and deprecated in Release 1.55 final. Their functionality is
459 now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
460
461 Bio.UniGene
462 ===========
463 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
464 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
465 Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release
466 1.55 final. Their functionality is now available through a read() and a parse()
467 function in Bio.UniGene.
815d64f making the obsolete classes more explicit
mdehoon authored
468
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