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1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
1 This file provides documentation for modules in Biopython that have been moved
2 or deprecated in favor of other modules. This provides some quick and easy
3 to find documentation about how to update your code to work again.
4
b4379ed @peterjc Dropping support for Python 2.3
peterjc authored
5 Python 2.3
6 ==========
7 No longer supported as of Release 1.51, having triggered a warning with
8 Release 1.50, with a mention in the release notes for Release 1.49.
9
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
10 Python 2.4
11 ==========
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).
0c51079 @peterjc Minor update to DEPRECATED file regarding Python 2.4
peterjc authored
17 An explicit warning was added to setup.py for Biopython 1.55 and 1.56.
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 DE...
peterjc authored
19 Bio.Encodings
20 =============
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
21 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
22 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
23
24 Bio.PropertyManager
25 ===================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
26 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
27 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
28
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
29 Bio.InterPro
30 ============
4749068 @peterjc Remove deprecated Bio.InterPro module (HTML parser)
peterjc authored
31 This module was a parser for the EBI InterPro webpages, but no longer worked
32 with their current website. Deprecated in Release 1.55, and removed in
33 Release 1.58.
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
34
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
35 Bio.GenBank.LocationParser
36 ==========================
37 This module used to be used for parsing GenBank and EMBL feature locations.
38 It has been replaced with faster code using regular expressions, and is no
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.spar...
peterjc authored
39 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 as...
peterjc authored
40
41 Bio.Parsers and Bio.Parsers.spark
42 =================================
43 This module was a copy of John Aycock's SPARK parser included with Biopython
f38249a @peterjc Fixed a typo
peterjc authored
44 soley for use in Bio.GenBank.LocationParser. Declared obsolete in Release
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.spar...
peterjc authored
45 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
46
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
47 Bio.Restriction.DNAUtils and check_bases
48 ========================================
49 This module (originally in C) offered complement and antiparallel functions
50 (duplicating functionality in Bio.Seq) and a rather odd function called
51 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
52 Deprecated in Release 1.53, removed in Release 1.57.
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
53
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
54 Bio.Blast.NCBIStandalone
55 ========================
56 The three functions for calling the "legacy" NCBI BLAST command line tools
57 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ad5ea06 @peterjc Clarify DEPRECATED file regarding application wrappers
peterjc authored
58 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 obsole...
peterjc authored
59
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
60 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
61 which was declared obsolete in Release 1.54. For some time now, both the NCBI
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
62 and Biopython have encouraged people to parse the XML output instead.
63
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
64 Bio.Blast.Applications
65 ======================
66 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
67 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
68 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
69 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
70
cbb051b @peterjc Note about the old EMBOSS PHYLIP wrappers being obsolete
peterjc authored
71 Bio.EMBOSS.Applications
72 =======================
73 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
74 obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
75 PHYLIP tools (e.g. fneighbor) instead.
76
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
77 Bio.Clustalw
78 ============
9cbdf28 @peterjc Remove deprecated Bio.Clustalw module
peterjc authored
79 Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
80 removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
81 clustal format alignments (since Release 1.46), and Bio.Align.Applications
82 for calling the ClustalW command line tool (since Release 1.51). See the
83 Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
84
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
85 BioSQL and psycopg
86 ==================
87 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
88 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
89
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
90 Bio.Application.generic_run and ApplicationResult
91 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
92 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
93 Release 1.57. Please use the Python subprocess module instead, or as of
94 Release 1.55 the application wrappers can be used directly to execute the
95 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
96
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
97 Bio.Entrez.efetch and rettype="genbank"
98 =======================================
99 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
100 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
101 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
102 automatically, but issues a deprecation warning. The code to check and correct
103 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
104
105 Bio.Entrez.query function
106 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
107 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
108
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
109 Bio.SwissProt.SProt
110 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
111 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
112 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
113 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
114
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
115 Bio.Prosite and Bio.Enzyme
116 ==========================
dcbdd45 @peterjc Removing deprecated Bio.Enzyme and Bio.Prosite modules
peterjc authored
117 Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in
118 Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and
04dcf21 @peterjc Minor correction to new module name
peterjc authored
119 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
120
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
121 Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredReader
122 ================================================
123 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredRe...
peterjc authored
124 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
125
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
126 Bio.File
127 ========
128 Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in
129 Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated
130 in Release 1.57.
131
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
132 Bio.Graphics.GenomeDiagram and colour/color, centre/center
133 ==========================================================
134 GenomeDiagram originally used colour and centre (UK spelling of color and
135 center) for argument names. As part of its integration into Biopython 1.50,
136 this will support both colour and color, and both centre and center, to help
137 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
138 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
139 intend to eventually remove support for colour and centre in later releases
140 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
141
142 Bio.AlignAce and Bio.MEME
143 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been rem...
peterjc authored
144 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
145 in Release 1.56. Please use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
146
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
147 Numeric support
148 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
149 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
150 Please move to NumPy for Biopython 1.49 or later.
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
151
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
152 Bio.Seq and the data property
153 =============================
154 Direct use of the Seq object (and MutableSeq object) .data property is
e5fbcd7 Issue a DeprecatingWarning when accessing the .data property of Seq obje...
Michiel de Hoon authored
155 deprecated. As of Release 1.49, writing to the Seq object's .data property
156 triggered a warning, and this property was made read only in Release 1.53. In
157 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 warning w...
peterjc authored
158
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
159 Bio.Transcribe and Bio.Translate
160 ================================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
161 Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
162 in Release 1.57. Please use the methods or functions in Bio.Seq instead.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
163
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
164 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
165 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and st...
peterjc authored
166 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
167 deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53.
e7f44b5 @peterjc Updated DEPRECATED file now that Bio.mathfns and Bio.stringfns have been...
peterjc authored
168 The three C implementations were all removed in Release 1.53. Bio.mathfns
7a92530 @peterjc Removed deprecated Bio.listfns module
peterjc authored
169 and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in
170 Release 1.57.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
171
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
172 Bio.distance (and Bio.cdistance)
173 ================================
174 Bio.distance was deprecated in Release 1.49, at which point its C code
175 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
176 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
177
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
178 Bio.Ndb
179 =======
180 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
181 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
182
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
183 Martel
184 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
185 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
186 in Release 1.51. The source code for Martel is still in our repository if
187 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
188
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
189 Bio.Mindy and associated modules.
190 =================================
191 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
192 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
193 Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.writ...
peterjc authored
194
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
195 Bio.Fasta index_file and Dictionary
196 ===================================
197 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
198 sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of
69f1dcc @peterjc Updated DEPRECATED file to reflect final name of Bio.SeqIO.index() funct...
peterjc authored
199 SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index()
8af957d @peterjc Adding the Bio.SeqIO.indexed_dict() function developed on a github branc...
peterjc authored
200 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
201
202 Bio.Fasta (including Bio.Fasta.FastaAlign)
203 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
204 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
205 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
206 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
207
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
208 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
209 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
210 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
211 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
212 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
213
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
214 Bio.Emboss.Primer
215 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Martel...
peterjc authored
216 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
217 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
218
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
219 Bio.Emboss.Applications
220 =======================
221 EProtDistCommandline, ENeighborCommandline, EProtParsCommandline,
222 EConsenseCommandline, and ESeqBootCommandline were declared obsolete in
223 Release 1.52, and deprecated in Release 1.55 final. These functions were
224 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
225 FConsenseCommandline, and FSeqBootCommandline, respectively.
226
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
227 Bio.MetaTool
228 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
229 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
230 for the output of MetaTool 3.5 which is now obsolete.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
231
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
232 Bio.GenBank
233 ===========
234 The online functionality (search_for, download_many, and NCBIDictionary) was
4f7d50c Removing the deprecated online bits of Bio.GenBank (replaced by Bio.Entr...
Peter Cock authored
235 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
236 in Release 1.54. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
237
238 Bio.PubMed
239 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
240 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
241 removed in Release 1.53. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
242
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
243 Bio.EUtils
244 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
245 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
246
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
247 Bio.Sequencing & Bio.Medline
248 ============================
249 A revised API was added and the old one deprecated in Release 1.48,
250 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
251 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
252 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
253 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
254 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
255 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
256 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
257
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
258 Bio.Blast.NCBIWWW
259 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
260 The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52.
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
261 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
262
263 Bio.Saf
264 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
265 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
266 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
267
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
268 Bio.NBRF
269 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
270 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
271 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
272
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
273 Bio.IntelliGenetics
274 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
275 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
276 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
277
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
278 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
279 =================================================================
280 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
281 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
282 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
283
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
284 Bio.SeqIO.to_alignment()
285 ========================
286 This function was made obsolete with the introduction of Bio.AlignIO,
9eb934e @peterjc Remove deprecated Bio.SeqIO.to_alignment function
peterjc authored
287 deprecated in Release 1.54, and removed in Release 1.58. Use either the
288 Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
289 directly instead.
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
290
5e507c9 Updating for release 1.47.
mdehoon authored
291 Bio.ECell
292 =========
293 Deprecated as of Release 1.47, as it appears to have no users, and the code
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
294 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
295
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
296 Bio.Ais
297 =======
298 Deprecated as of Release 1.45, removed in Release 1.49.
299
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
300 Bio.LocusLink
301 =============
302 Deprecated as of Release 1.45, removed in Release 1.49.
303 The NCBI's LocusLink was superseded by Entrez Gene.
304
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
305 Bio.SGMLExtractor
306 =================
307 Deprecated as of Release 1.46, removed in Release 1.49.
308
d01c450 Getting ready for release 1.46.
mdehoon authored
309 Bio.Rebase
310 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
311 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
312
313 Bio.Gobase
314 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
315 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
316
317 Bio.CDD
318 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
319 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
320
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
321 Bio.biblio
322 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
323 Deprecated as of Release 1.45, removed in Release 1.48
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
324
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
325 Bio.WWW
326 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
327 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
328 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
329 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
330
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bio.W...
peterjc authored
331 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
332 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
333 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
334
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
335 Bio.SeqIO
336 =========
337 The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
338 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
339
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
340 Bio.Medline.NLMMedlineXML
341 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
342 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
343
344 Bio.MultiProc
345 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
346 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
347
348 Bio.MarkupEditor
349 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
350 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
351
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
352 Bio.lcc
353 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
354 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
355
356 Bio.crc
357 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
358 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
359
360 Bio.FormatIO
361 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
362 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
363
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
364 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
365 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
366 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
367
368 Bio.Kabat
369 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
370 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
371
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
372 Bio.SeqUtils
373 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
374 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
375 in Release 1.31, and removed in Release 1.43. Function 'translate' was
376 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
377 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
378
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
379 Function makeTableX and classes ProteinX and MissingTable were deprecated
4804f1b @peterjc Remove deprecated makeTableX function and associated classes
peterjc authored
380 in Release 1.54, and removed in Release 1.58. These were remnants of the
381 removed translate function, and no longer served any useful purpose.
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
382
3178311 @peterjc Remove deprecated SeqUtils reverse function
peterjc authored
383 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
384 removed in Release 1.58. Instead just use the string's slice method with
385 a step of minus one.
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
386
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
387 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
b6fd79e @peterjc Remove more deprecated functions in Bio.SeqUtils
peterjc authored
388 quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
389 in Release 1.58.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
390
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
391 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
392 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
393 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
394 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
395 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
396
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
397 The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
398 in Release 1.57 (with the intention of reusing this name space for a GFF
399 parser).
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
400
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
401 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
402 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
403 Deprecated as of Release 1.30, removed in Release 1.42.
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
404 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
405
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
406 Bio.SVM
407 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
408 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
409 The Support Vector Machine code in Biopython has been superceeded by a
410 more robust (and maintained) SVM library, which includes a python
411 interface. We recommend using LIBSVM:
412
413 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
414
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
415 Bio.RecordFile
416 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
417 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
418 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
419
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
420 Bio.kMeans and Bio.xkMeans
421 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
422 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
423 the function kcluster in Bio.Cluster which performs k-means or k-medians
424 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
425
426 Bio.InterPro
427 ============
428 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
429 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
430
431 Bio.SCOP
432 ========
433 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
434 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
435 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
436
437 Bio.utils
438 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
439 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
440 and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
ca87378 @peterjc Adding a note to the Bio.utils section of the DEPRECATED file that this ...
peterjc authored
441 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
442 The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
443 Release 1.56, and removed in Release 1.57.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
444
445 Bio.Motif
446 =========
447 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
448 declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
449 in Release 1.57.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
450 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
451 in Release 1.53 and deprecated in Release 1.55 final; their functionality is
40ff78e Updating the DEPRECATED file concerning the parser simplifications in Bi...
mdehoon authored
452 now available through a read() function in Bio.Motif.Parsers.AlignAce.
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
453 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
454 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
455 deprecated in Release 1.55 final; their functionality is now available through
456 a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
457 respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace RecordPa...
mdehoon authored
458
459 Bio.Compass
460 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
461 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
462 and deprecated in Release 1.55 final. Their functionality is now available
463 through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
464
465 Bio.Affy.CelFile
466 ================
467 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
468 in Release 1.54. Their functionality is now available through a read()
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
469 function. These classes were deprecated in Release 1.55 final.
815d64f making the obsolete classes more explicit
mdehoon authored
470
471 Bio.PopGen.FDist
472 ================
473 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
f70cc43 Adding DeprecationWarnings to obsolete code in Bio.PopGen.FDist. Applyin...
Michiel de Hoon authored
474 in Release 1.54, and deprecated in Release 1.55 final. Their functionality is
475 now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
476
477 Bio.UniGene
478 ===========
479 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
480 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
481 Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release
482 1.55 final. Their functionality is now available through a read() and a parse()
483 function in Bio.UniGene.
815d64f making the obsolete classes more explicit
mdehoon authored
484
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
485 Bio.SubsMat
486 ===========
487 The methods letter_sum and all_letters_sum were removed from the SeqMat class in
488 Bio.SubsMat in Release 1.57.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
489
490 Bio.Align
491 =========
492 The methods get_column and add_sequence of the MultipleSeqAlignment class were
493 deprecated in Release 1.57. The Alignment class in Bio.Align.Generic and its
494 method get_seq_by_num were deprecated in Release 1.57.
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