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