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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 =============
21 Declared obsolete in Release 1.55.
22
23 Bio.PropertyManager
24 ===================
25 Declared obsolete in Biopython 1.55.
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
5008913 @peterjc Fixed typo
peterjc authored
36 longer needed. Declared obsolete in Release 1.55.
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
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
42 1.55.
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).
49 Deprecated in Release 1.53.
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 =================================================
2c7126b @peterjc Updating DEPRECATED file regarding Bio.Application and Bio.WWW
peterjc authored
88 Declared obsolete in Release 1.51, and deprecated in Release 1.53.
ad5ea06 @peterjc Clarify DEPRECATED file regarding application wrappers
peterjc authored
89 Please use the Python subprocess module instead, of as of Release 1.55 the
90 application wrappers can be used directly to execute the command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
91
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
92 Bio.Entrez.efetch and rettype="genbank"
93 =======================================
94 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
95 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
96 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
97 automatically, but issues a deprecation warning. The code to check and correct
98 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
99
100 Bio.Entrez.query function
101 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
102 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
103
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
104 Bio.SwissProt.SProt
105 ===================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
106 Declared obsolete in Release 1.50, and deprecated in Release 1.51. Most of the
107 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
108
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
109 Bio.Prosite and Bio.Enzyme
110 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
111 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
112 Most of the functionality has moved to Bio.ExPASy.Prosite and
113 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
114
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
115 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
116 =====================================================================
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.Filtere…
peterjc authored
117 Declared obsolete in Release 1.50, deprecated in Release 1.52, removed in
118 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
119
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
120 Bio.Graphics.GenomeDiagram and colour/color, centre/center
121 ==========================================================
122 GenomeDiagram originally used colour and centre (UK spelling of color and
123 center) for argument names. As part of its integration into Biopython 1.50,
124 this will support both colour and color, and both centre and center, to help
125 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
126 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
127 intend to eventually remove support for colour and centre in later releases
128 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
129
130 Bio.AlignAce and Bio.MEME
131 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been …
peterjc authored
132 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
133 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
134
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
135 Numeric support
136 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
137 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
138 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
139
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
140 Bio.Seq and the data property
141 =============================
142 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
143 deprecated. As of Release 1.49, writing to the Seq object's .data property
144 triggered a warning, and this property was made read only in Release 1.53. In
145 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
146
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
147 Bio.Transcribe and Bio.Translate
148 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
149 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
150 Please use the methods or functions in Bio.Seq instead.
151
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
152 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
153 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and…
peterjc authored
154 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
155 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
156 The three C implementations were all removed in Release 1.53. Bio.mathfns
157 and Bio.stringfns were removed in Release 1.55.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
158
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
159 Bio.distance (and Bio.cdistance)
160 ================================
161 Bio.distance was deprecated in Release 1.49, at which point its C code
162 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
163 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
164
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
165 Bio.Ndb
166 =======
167 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
168 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
169
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
170 Martel
171 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
172 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
173 in Release 1.51. The source code for Martel is still in our repository if
174 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
175
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
176 Bio.Mindy and associated modules.
177 =================================
178 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
179 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
180 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
181
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
182 Bio.Fasta index_file and Dictionary
183 ===================================
184 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
185 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
186 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
187 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
188
189 Bio.Fasta (including Bio.Fasta.FastaAlign)
190 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
191 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
192 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
193 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
194
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
195 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
196 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
197 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
198 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
199 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
200
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
201 Bio.Emboss.Primer
202 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
203 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
204 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
205
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
206 Bio.Emboss.Applications
207 =======================
208 EProtDistCommandline, ENeighborCommandline, EProtParsCommandline,
209 EConsenseCommandline, and ESeqBootCommandline were declared obsolete in
210 Release 1.52, and deprecated in Release 1.55 final. These functions were
211 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
212 FConsenseCommandline, and FSeqBootCommandline, respectively.
213
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
214 Bio.MetaTool
215 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
216 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
217 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
218
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
219 Bio.GenBank
220 ===========
221 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
222 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
223 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
224
225 Bio.PubMed
226 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
227 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
228 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
229
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
230 Bio.EUtils
231 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
232 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
233
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
234 Bio.Sequencing & Bio.Medline
235 ============================
236 A revised API was added and the old one deprecated in Release 1.48,
237 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
238 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
239 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
240 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
241 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
242 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
243 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
244
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
245 Bio.Blast.NCBIWWW
246 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
247 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
248 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
249
250 Bio.Saf
251 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
252 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
253 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
254
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
255 Bio.NBRF
256 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
257 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
258 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
259
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
260 Bio.IntelliGenetics
261 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
262 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
263 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
264
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
265 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
266 =================================================================
267 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
268 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
269 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
270
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
271 Bio.SeqIO.to_alignment()
272 ========================
273 This function was made obsolete with the introduction of Bio.AlignIO,
274 and deprecated in Release 1.54. Use either the Bio.AlignIO functions,
275 or the Bio.Align.MultipleSeqAlignment class directly instead.
276
5e507c9 Updating for release 1.47.
mdehoon authored
277 Bio.ECell
278 =========
279 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
280 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
281
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
282 Bio.Ais
283 =======
284 Deprecated as of Release 1.45, removed in Release 1.49.
285
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
286 Bio.LocusLink
287 =============
288 Deprecated as of Release 1.45, removed in Release 1.49.
289 The NCBI's LocusLink was superseded by Entrez Gene.
290
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
291 Bio.SGMLExtractor
292 =================
293 Deprecated as of Release 1.46, removed in Release 1.49.
294
d01c450 Getting ready for release 1.46.
mdehoon authored
295 Bio.Rebase
296 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
297 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
298
299 Bio.Gobase
300 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
301 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
302
303 Bio.CDD
304 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
305 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
306
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
307 Bio.biblio
308 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
309 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
310
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
311 Bio.WWW
312 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
313 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
314 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
315 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
316
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bi…
peterjc authored
317 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
318 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
319 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
320
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
321 Bio.SeqIO
322 =========
323 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
324 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
325
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
326 Bio.Medline.NLMMedlineXML
327 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
328 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
329
330 Bio.MultiProc
331 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
332 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
333
334 Bio.MarkupEditor
335 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
336 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
337
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
338 Bio.lcc
339 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
340 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
341
342 Bio.crc
343 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
344 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
345
346 Bio.FormatIO
347 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
348 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
349
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
350 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
351 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
352 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
353
354 Bio.Kabat
355 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
356 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
357
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
358 Bio.SeqUtils
359 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
360 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
361 in Release 1.31, and removed in Release 1.43. Function 'translate' was
362 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
363 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
364
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
365 Function makeTableX and classes ProteinX and MissingTable were deprecated
366 in Release 1.54. These were remnants of the removed translate function,
367 and no longer served any useful purpose.
368
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
369 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
370 just use the string's slice method with a step of minus one.
371
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
372 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
373 quicker_apply_on_multi_fasta were deprecated in Release 1.55 final.
374
375
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
376 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
377 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
378 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
379 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
380 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
381
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
382 The whole of the old Bio.GFF module was deprecated in Release 1.53
383 (with the intention of reusing this name space for a GFF parser).
384
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
385 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
386 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
387 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
388 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
389
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
390 Bio.SVM
391 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
392 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
393 The Support Vector Machine code in Biopython has been superceeded by a
394 more robust (and maintained) SVM library, which includes a python
395 interface. We recommend using LIBSVM:
396
397 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
398
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
399 Bio.RecordFile
400 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
401 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
402 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
403
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
404 Bio.kMeans and Bio.xkMeans
405 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from B…
peterjc authored
406 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
407 the function kcluster in Bio.Cluster which performs k-means or k-medians
408 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
409
410 Bio.InterPro
411 ============
412 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
413 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
414
415 Bio.SCOP
416 ========
417 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
b59b285 Removing the deprecated class Parser from Bio.SCOP.Dom
Michiel de Hoon authored
418 Release 1.53. The class Parser in Bio.SCOP.DOM was removed in Release 1.55
419 final.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
420
421 Bio.utils
422 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
423 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
424 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
425 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
426 The whole of Bio.utils was declared obsolete in Release 1.55.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
427
428 Bio.Motif
429 =========
430 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
431 declared obsolete in Release 1.53, and deprecated in Release 1.55 final.
432 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
433 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
434 now available through a read() function in Bio.Motif.Parsers.AlignAce.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
435 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser, _MASTScanner,
436 and MASTRecord were declared obsolete in Release 1.54 and deprecated in Release
437 1.55 final; their functionality is now available through a read() function in
815d64f making the obsolete classes more explicit
mdehoon authored
438 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
439
440 Bio.Compass
441 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
442 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
443 and deprecated in Release 1.55 final. Their functionality is now available
444 through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
445
446 Bio.Affy.CelFile
447 ================
448 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
449 in Release 1.54. Their functionality is now available through a read()
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
450 function. These classes were deprecated in Release 1.55 final.
815d64f making the obsolete classes more explicit
mdehoon authored
451
452 Bio.PopGen.FDist
453 ================
454 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
f70cc43 Adding DeprecationWarnings to obsolete code in Bio.PopGen.FDist. Appl…
Michiel de Hoon authored
455 in Release 1.54, and deprecated in Release 1.55 final. Their functionality is
456 now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
457
458 Bio.UniGene
459 ===========
460 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
461 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
462 Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release
463 1.55 final. Their functionality is now available through a read() and a parse()
464 function in Bio.UniGene.
815d64f making the obsolete classes more explicit
mdehoon authored
465
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