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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
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI I…
peterjc authored
19 Bio.InterPro
20 ============
21 This module was a parser for the EBI InterPro webpages, but no longer works
22 with their current website. Deprecated in Release 1.55.
23
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
24 Bio.GenBank.LocationParser
25 ==========================
26 This module used to be used for parsing GenBank and EMBL feature locations.
27 It has been replaced with faster code using regular expressions, and is no
28 longer needed. Declated obsolete in Release 1.55.
29
30 Bio.Parsers and Bio.Parsers.spark
31 =================================
32 This module was a copy of John Aycock's SPARK parser included with Biopython
33 soley for use in Bio.GenBank.LocationParser. Declated obsolete in Release
34 1.55.
35
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
36 Bio.Restriction.DNAUtils and check_bases
37 ========================================
38 This module (originally in C) offered complement and antiparallel functions
39 (duplicating functionality in Bio.Seq) and a rather odd function called
40 check_bases (also available as Bio.Restriction.Restriction.check_bases).
41 Deprecated in Release 1.53.
42
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
43 Bio.Blast.NCBIStandalone
44 ========================
45 The three functions for calling the "legacy" NCBI BLAST command line tools
46 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
47 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications and the Python
48 subprocess module instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
49
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
50 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
51 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
52 and Biopython have encouraged people to parse the XML output instead.
53
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
54 Bio.Blast.Applications
55 ======================
56 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
57 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
58 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
59 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as o…
peterjc authored
60
cbb051b @peterjc Note about the old EMBOSS PHYLIP wrappers being obsolete
peterjc authored
61 Bio.EMBOSS.Applications
62 =======================
63 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
64 obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
65 PHYLIP tools (e.g. fneighbor) instead.
66
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
67 Bio.Clustalw
68 ============
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
69 Declared obsolete in Release 1.52, and deprecated in Release 1.55 final,
70 having been replaced with Bio.AlignIO for parsing and writing clustal format
71 alignments (since Release 1.46), and Bio.Align.Applications for calling the
72 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
73
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
74 BioSQL and psycopg
75 ==================
76 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
77 in Release 1.51, please use psycopg2 instead.
78
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
79 Bio.Application.generic_run and ApplicationResult
80 =================================================
2c7126b @peterjc Updating DEPRECATED file regarding Bio.Application and Bio.WWW
peterjc authored
81 Declared obsolete in Release 1.51, and deprecated in Release 1.53.
82 Please use the Python subprocess module instead.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
83
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
84 Bio.Entrez.efetch and rettype="genbank"
85 =======================================
86 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
87 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
88 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
89 automatically, but issues a deprecation warning. The code to check and correct
90 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
91
92 Bio.Entrez.query function
93 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
94 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
95
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
96 Bio.SwissProt.SProt
97 ===================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
98 Declared obsolete in Release 1.50, and deprecated in Release 1.51. Most of the
99 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
100
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
101 Bio.Prosite and Bio.Enzyme
102 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
103 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
104 Most of the functionality has moved to Bio.ExPASy.Prosite and
105 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
106
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
107 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
108 =====================================================================
bc953fa @peterjc Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio…
peterjc authored
109 Declared obsolete in Release 1.50, deprecated in Release 1.52.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
110
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
111 Bio.Graphics.GenomeDiagram and colour/color, centre/center
112 ==========================================================
113 GenomeDiagram originally used colour and centre (UK spelling of color and
114 center) for argument names. As part of its integration into Biopython 1.50,
115 this will support both colour and color, and both centre and center, to help
116 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
117 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
118 intend to eventually remove support for colour and centre in later releases
119 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
120
121 Bio.AlignAce and Bio.MEME
122 =========================
e62220a @peterjc Deprecation warnings for Bio.AlignAce and Bio.MEME
peterjc authored
123 Declared obsolete in Release 1.50, and deprecated in Release 1.52. Please
124 use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
125
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
126 Numeric support
127 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
128 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
129 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
130
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
131 Bio.Seq and the data property
132 =============================
133 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
134 deprecated. As of Release 1.49, writing to the Seq object's .data property
135 triggered a warning, and this property was made read only in Release 1.53. In
136 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
137
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
138 Bio.Transcribe and Bio.Translate
139 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
140 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
141 Please use the methods or functions in Bio.Seq instead.
142
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
143 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
144 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and…
peterjc authored
145 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
146 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
147 The three C implementations were all removed in Release 1.53. Bio.mathfns
148 and Bio.stringfns were removed in Release 1.55.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
149
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
150 Bio.distance (and Bio.cdistance)
151 ================================
152 Bio.distance was deprecated in Release 1.49, at which point its C code
153 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
154 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
155
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
156 Bio.Ndb
157 =======
158 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
159 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
160
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
161 Martel
162 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
163 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
164 in Release 1.51. The source code for Martel is still in our repository if
165 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
166
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
167 Bio.Mindy and associated modules.
168 =================================
169 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
170 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
171 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
172
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
173 Bio.Fasta index_file and Dictionary
174 ===================================
175 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
176 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
177 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
178 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
179
180 Bio.Fasta (including Bio.Fasta.FastaAlign)
181 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
182 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
183 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
184 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
185
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
186 Bio.Align.FormatConvert
187 =======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
188 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
189 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
190 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
191
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
192 Bio.Emboss.Primer
193 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
194 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
195 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
196
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
197 Bio.Emboss.Applications
198 =======================
199 EProtDistCommandline, ENeighborCommandline, EProtParsCommandline,
200 EConsenseCommandline, and ESeqBootCommandline were declared obsolete in
201 Release 1.52, and deprecated in Release 1.55 final. These functions were
202 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
203 FConsenseCommandline, and FSeqBootCommandline, respectively.
204
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
205 Bio.MetaTool
206 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
207 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
208 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
209
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
210 Bio.GenBank
211 ===========
212 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
213 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
214 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
215
216 Bio.PubMed
217 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
218 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
219 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
220
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
221 Bio.EUtils
222 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
223 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
224
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
225 Bio.Sequencing & Bio.Medline
226 ============================
227 A revised API was added and the old one deprecated in Release 1.48,
228 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
229 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
230 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
231 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
232 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
233 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
234 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
235
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
236 Bio.Blast.NCBIWWW
237 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
238 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
239 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
240
241 Bio.Saf
242 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
243 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
244 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
245
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
246 Bio.NBRF
247 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
248 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
249 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
250
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
251 Bio.IntelliGenetics
252 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
253 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
254 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
255
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
256 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
257 =================================================================
258 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
259 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
260 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
261
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
262 Bio.SeqIO.to_alignment()
263 ========================
264 This function was made obsolete with the introduction of Bio.AlignIO,
265 and deprecated in Release 1.54. Use either the Bio.AlignIO functions,
266 or the Bio.Align.MultipleSeqAlignment class directly instead.
267
5e507c9 Updating for release 1.47.
mdehoon authored
268 Bio.ECell
269 =========
270 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
271 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
272
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
273 Bio.Ais
274 =======
275 Deprecated as of Release 1.45, removed in Release 1.49.
276
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
277 Bio.LocusLink
278 =============
279 Deprecated as of Release 1.45, removed in Release 1.49.
280 The NCBI's LocusLink was superseded by Entrez Gene.
281
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
282 Bio.SGMLExtractor
283 =================
284 Deprecated as of Release 1.46, removed in Release 1.49.
285
d01c450 Getting ready for release 1.46.
mdehoon authored
286 Bio.Rebase
287 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
288 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
289
290 Bio.Gobase
291 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
292 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
293
294 Bio.CDD
295 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
296 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
297
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
298 Bio.biblio
299 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
300 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
301
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
302 Bio.WWW
303 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
304 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
305 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
306 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
307
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bi…
peterjc authored
308 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
309 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
310 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
311
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
312 Bio.SeqIO
313 =========
314 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
315 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
316
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
317 Bio.Medline.NLMMedlineXML
318 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
319 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
320
321 Bio.MultiProc
322 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
323 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
324
325 Bio.MarkupEditor
326 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
327 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
328
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
329 Bio.lcc
330 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
331 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
332
333 Bio.crc
334 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
335 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
336
337 Bio.FormatIO
338 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
339 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
340
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
341 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
342 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
343 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
344
345 Bio.Kabat
346 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
347 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
348
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
349 Bio.SeqUtils
350 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
351 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
352 in Release 1.31, and removed in Release 1.43. Function 'translate' was
353 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
354 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
355
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
356 Function makeTableX and classes ProteinX and MissingTable were deprecated
357 in Release 1.54. These were remnants of the removed translate function,
358 and no longer served any useful purpose.
359
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
360 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
361 just use the string's slice method with a step of minus one.
362
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
363 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
364 quicker_apply_on_multi_fasta were deprecated in Release 1.55 final.
365
366
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
367 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
368 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
369 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
370 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
371 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
372
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
373 The whole of the old Bio.GFF module was deprecated in Release 1.53
374 (with the intention of reusing this name space for a GFF parser).
375
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
376 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
377 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
378 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
379 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
380
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
381 Bio.SVM
382 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
383 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
384 The Support Vector Machine code in Biopython has been superceeded by a
385 more robust (and maintained) SVM library, which includes a python
386 interface. We recommend using LIBSVM:
387
388 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
389
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
390 Bio.RecordFile
391 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
392 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
393 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
394
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
395 Bio.kMeans and Bio.xkMeans
396 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
397 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
398 the function kcluster in Bio.Cluster which performs k-means or k-medians
399 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
400
401 Bio.InterPro
402 ============
403 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
404 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
405
406 Bio.SCOP
407 ========
408 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
409 Release 1.53.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
410
411 Bio.utils
412 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
413 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
414 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
415 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
416
417 Bio.Motif
418 =========
419 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
420 declared obsolete in Release 1.53, and deprecated in Release 1.55 final.
421 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
422 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
423 now available through a read() function in Bio.Motif.Parsers.AlignAce.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
424 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser, _MASTScanner,
425 and MASTRecord were declared obsolete in Release 1.54 and deprecated in Release
426 1.55 final; their functionality is now available through a read() function in
815d64f making the obsolete classes more explicit
mdehoon authored
427 Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST, respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace Recor…
mdehoon authored
428
429 Bio.Compass
430 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
431 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
432 and deprecated in Release 1.55 final. Their functionality is now available
433 through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
434
435 Bio.Affy.CelFile
436 ================
437 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
438 in Release 1.54. Their functionality is now available through a read()
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
439 function. These classes were deprecated in Release 1.55 final.
815d64f making the obsolete classes more explicit
mdehoon authored
440
441 Bio.PopGen.FDist
442 ================
443 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
f70cc43 Adding DeprecationWarnings to obsolete code in Bio.PopGen.FDist. Appl…
Michiel de Hoon authored
444 in Release 1.54, and deprecated in Release 1.55 final. Their functionality is
445 now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
446
447 Bio.UniGene
448 ===========
449 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
450 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
451 Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release
452 1.55 final. Their functionality is now available through a read() and a parse()
453 function in Bio.UniGene.
815d64f making the obsolete classes more explicit
mdehoon authored
454
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