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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 ==========
9cdfacb @peterjc Clarify Python 2.4 status in DEPRECATED file
peterjc authored
12 No longer supported as of Release 1.59, having triggered a warning since
13 Release 1.55, with advance notice in the release notes for Release 1.54.
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
14
3f17f75 @peterjc We are phasing out support for Python 2.5
peterjc authored
15 Python 2.5
16 ==========
17 Still supported, but has triggered a warning since Release 1.61.
18
e5ff9e4 @peterjc Talk about CompoundLocation and sub_features in DEPRECATED file
peterjc authored
19 Bio.SeqFeature
20 ==============
21 With the introduction of the CompoundLocation in Release 1.62, the SeqFeature
22 attribute sub_features was deprecated.
23
316c42a @peterjc Deprecate Bio.SeqIO.Interfaces class InterlacedSequenceIterator
peterjc authored
24 Bio.SeqIO.Interfaces
25 ====================
26 Unused class InterlacedSequenceIterator was deprecated in Release 1.61.
27
965dcf6 @semenko Deprecate Bio/HotRand.py
semenko authored
28 Bio.HotRand
29 ===========
30 Obsolete file Bio/HotRand.py was deprecated in Release 1.61, consider using
31 an alternative RNG, or the Python module "randomdotorg".
32
5a275cc @peterjc Formerly deprecate long obsolete file Bio/Search.py
peterjc authored
33 Bio.Search
34 ==========
35 Long obsolete file Bio/Search.py was deprecated in Release 1.61.
36
cbc7c87 @peterjc Deprecate Bio.Pathway.Rep.HashSet, use set instead.
peterjc authored
37 Bio.Pathway.Rep.HashSet
38 =======================
39 Deprecated in Release 1.59, use Python's built in set module.
40
c52e986 @peterjc Make Bio.SeqFeature position objects act like and subclass int
peterjc authored
41 Bio.SeqFeature.WithinPosition and OneOfPosition
42 ===============================================
43 The arguments to create these fuzzy positions changed in Release 1.59.
44
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
45 Bio.Encodings
46 =============
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
47 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
48 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
49
50 Bio.PropertyManager
51 ===================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
52 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
53 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
54
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI I…
peterjc authored
55 Bio.InterPro
56 ============
4749068 @peterjc Remove deprecated Bio.InterPro module (HTML parser)
peterjc authored
57 This module was a parser for the EBI InterPro webpages, but no longer worked
58 with their current website. Deprecated in Release 1.55, and removed in
59 Release 1.58.
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI I…
peterjc authored
60
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
61 Bio.GenBank.LocationParser
62 ==========================
63 This module used to be used for parsing GenBank and EMBL feature locations.
64 It has been replaced with faster code using regular expressions, and is no
53d44f9 @peterjc Remove deprecated Bio.Parsers and Bio.GenBank.LocationParser
peterjc authored
65 longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56,
66 and removed in Release 1.59.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
67
68 Bio.Parsers and Bio.Parsers.spark
69 =================================
70 This module was a copy of John Aycock's SPARK parser included with Biopython
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
71 solely for use in Bio.GenBank.LocationParser. Declared obsolete in Release
53d44f9 @peterjc Remove deprecated Bio.Parsers and Bio.GenBank.LocationParser
peterjc authored
72 1.55, deprecated in Release 1.56, and removed in Release 1.59.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers…
peterjc authored
73
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
74 Bio.Restriction.DNAUtils and check_bases
75 ========================================
76 This module (originally in C) offered complement and antiparallel functions
77 (duplicating functionality in Bio.Seq) and a rather odd function called
78 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
79 Deprecated in Release 1.53, removed in Release 1.57.
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
80
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
81 Bio.Blast.NCBIStandalone
82 ========================
83 The three functions for calling the "legacy" NCBI BLAST command line tools
84 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
85 1.53, and deprecated in Release 1.61. Please use the BLAST+ wrappers in
86 Bio.Blast.Applications instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
87
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
88 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
89 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
90 and Biopython have encouraged people to parse the XML output instead.
91
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
92 Bio.Blast.Applications
93 ======================
94 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
95 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
96 1.53 and deprecated in Release 1.61, having been replaced with wrappers for
97 the new NCBI BLAST+ tools (e.g. NcbiblastpCommandline and
98 NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as o…
peterjc authored
99
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
100 Bio.Clustalw
101 ============
9cbdf28 @peterjc Remove deprecated Bio.Clustalw module
peterjc authored
102 Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
103 removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
104 clustal format alignments (since Release 1.46), and Bio.Align.Applications
105 for calling the ClustalW command line tool (since Release 1.51). See the
106 Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
107
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
108 BioSQL and psycopg
109 ==================
110 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
111 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
112
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
113 Bio.Application.generic_run and ApplicationResult
114 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
115 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
116 Release 1.57. Please use the Python subprocess module instead, or as of
117 Release 1.55 the application wrappers can be used directly to execute the
118 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
119
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
120 Bio.Entrez.efetch and rettype="genbank"
121 =======================================
122 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
123 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
124 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
125 automatically, but issues a deprecation warning. The code to check and correct
126 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
127
128 Bio.Entrez.query function
129 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
130 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
131
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
132 Bio.SwissProt.SProt
133 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
134 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
135 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
136 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
137
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
138 Bio.Prosite and Bio.Enzyme
139 ==========================
dcbdd45 @peterjc Removing deprecated Bio.Enzyme and Bio.Prosite modules
peterjc authored
140 Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in
141 Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and
04dcf21 @peterjc Minor correction to new module name
peterjc authored
142 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
143
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
144 Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredReader
145 ================================================
146 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.Filtere…
peterjc authored
147 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
148
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
149 Bio.File
150 ========
151 Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in
152 Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated
084c898 @peterjc Remove deprecated Bio.File.StringHandle and SGMLStripper
peterjc authored
153 in Release 1.57, removed in Release 1.61. Bio.File.StringHandle was deprecated
154 in Release 1.59, removed in Release 1.61.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
155
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
156 Bio.Graphics.GenomeDiagram and colour/color, centre/center
157 ==========================================================
158 GenomeDiagram originally used colour and centre (UK spelling of color and
159 center) for argument names. As part of its integration into Biopython 1.50,
160 this will support both colour and color, and both centre and center, to help
161 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
162 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
163 intend to eventually remove support for colour and centre in later releases
164 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
165
166 Bio.AlignAce and Bio.MEME
167 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been …
peterjc authored
168 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
169 in Release 1.56. Please use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
170
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
171 Numeric support
172 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
173 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
174 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
175
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
176 Bio.Seq and the data property
177 =============================
178 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
179 deprecated. As of Release 1.49, writing to the Seq object's .data property
180 triggered a warning, and this property was made read only in Release 1.53. In
181 Release 1.55 final, accessing the .data property gives a DeprecationWarning.
e3cf12a @peterjc Remove the deprecated Seq object's data property
peterjc authored
182 The Seq object's .data property was removed in Release 1.61.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warnin…
peterjc authored
183
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
184 Bio.Transcribe and Bio.Translate
185 ================================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
186 Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
187 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 …
peterjc authored
188
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
189 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
190 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and…
peterjc authored
191 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
192 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
193 The three C implementations were all removed in Release 1.53. Bio.mathfns
7a92530 @peterjc Removed deprecated Bio.listfns module
peterjc authored
194 and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in
195 Release 1.57.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
196
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
197 Bio.distance (and Bio.cdistance)
198 ================================
199 Bio.distance was deprecated in Release 1.49, at which point its C code
200 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
201 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
202
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
203 Bio.Ndb
204 =======
205 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
206 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
207
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
208 Martel
209 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
210 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
211 in Release 1.51. The source code for Martel is still in our repository if
212 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
213
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
214 Bio.Mindy and associated modules.
215 =================================
216 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
217 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
218 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
219
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
220 Bio.Fasta index_file and Dictionary
221 ===================================
222 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
223 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
224 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
225 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
226
227 Bio.Fasta (including Bio.Fasta.FastaAlign)
228 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
229 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
230 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
231 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
232
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
233 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in…
peterjc authored
234 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
235 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
236 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
237 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
238
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
239 Bio.Emboss.Primer
240 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
241 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
242 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
243
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
244 Bio.Emboss.Applications
245 =======================
53f4841 @peterjc Remove deprecated EMBOSS PHYLIP wrappers
peterjc authored
246 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
247 obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in
248 release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g.
249 fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline,
250 EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
251 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
252 FConsenseCommandline, and FSeqBootCommandline, respectively.
253
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
254 Bio.MetaTool
255 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
256 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
257 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
258
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
259 Bio.GenBank
260 ===========
261 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
262 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
263 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
264
265 Bio.PubMed
266 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
267 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
268 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
269
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
270 Bio.EUtils
271 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
272 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
273
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
274 Bio.Sequencing & Bio.Medline
275 ============================
276 A revised API was added and the old one deprecated in Release 1.48,
277 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
278 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
279 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
280 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
281 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
282 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
283 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
284
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
285 Bio.Blast.NCBIWWW
286 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
287 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
288 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
289
290 Bio.Saf
291 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
292 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
293 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
294
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
295 Bio.NBRF
296 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
297 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
298 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
299
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
300 Bio.IntelliGenetics
301 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
302 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
303 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
304
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
305 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
306 =================================================================
307 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
308 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
309 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
310
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
311 Bio.SeqIO.to_alignment()
312 ========================
313 This function was made obsolete with the introduction of Bio.AlignIO,
9eb934e @peterjc Remove deprecated Bio.SeqIO.to_alignment function
peterjc authored
314 deprecated in Release 1.54, and removed in Release 1.58. Use either the
315 Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
316 directly instead.
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
317
5e507c9 Updating for release 1.47.
mdehoon authored
318 Bio.ECell
319 =========
320 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
321 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
322
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
323 Bio.Ais
324 =======
325 Deprecated as of Release 1.45, removed in Release 1.49.
326
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
327 Bio.LocusLink
328 =============
329 Deprecated as of Release 1.45, removed in Release 1.49.
330 The NCBI's LocusLink was superseded by Entrez Gene.
331
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
332 Bio.SGMLExtractor
333 =================
334 Deprecated as of Release 1.46, removed in Release 1.49.
335
d01c450 Getting ready for release 1.46.
mdehoon authored
336 Bio.Rebase
337 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
338 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
339
340 Bio.Gobase
341 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
342 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
343
344 Bio.CDD
345 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
346 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
347
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
348 Bio.biblio
349 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
350 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
351
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
352 Bio.WWW
353 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
354 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
355 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
356 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
357
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bi…
peterjc authored
358 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
359 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
360 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
361
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
362 Bio.SeqIO
363 =========
364 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
365 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
366
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
367 Bio.Medline.NLMMedlineXML
368 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
369 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
370
371 Bio.MultiProc
372 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
373 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
374
375 Bio.MarkupEditor
376 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
377 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
378
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
379 Bio.lcc
380 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
381 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
382
383 Bio.crc
384 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
385 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
386
387 Bio.FormatIO
388 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
389 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
390
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
391 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
392 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
393 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
394
395 Bio.Kabat
396 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
397 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
398
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
399 Bio.SeqUtils
400 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
401 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
402 in Release 1.31, and removed in Release 1.43. Function 'translate' was
403 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
404 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
405
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
406 Function makeTableX and classes ProteinX and MissingTable were deprecated
4804f1b @peterjc Remove deprecated makeTableX function and associated classes
peterjc authored
407 in Release 1.54, and removed in Release 1.58. These were remnants of the
408 removed translate function, and no longer served any useful purpose.
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
409
3178311 @peterjc Remove deprecated SeqUtils reverse function
peterjc authored
410 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
411 removed in Release 1.58. Instead just use the string's slice method with
412 a step of minus one.
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
413
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
414 Functions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
b6fd79e @peterjc Remove more deprecated functions in Bio.SeqUtils
peterjc authored
415 quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
416 in Release 1.58.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
417
3798b78 @peterjc Note quick_FASTA_reader -> SimpleFastaParser in DEPRECATED file
peterjc authored
418 Function quick_FASTA_reader was declared obsolete in Release 1.61. Use
419 function list(SimpleFastaParser(handle)) in Bio.SeqIO.FastaIO instead
420 (but ideally convert your code to using an iterator approach).
239b739 @peterjc Add a doctest to quick_FASTA_reader, declare it obsolete
peterjc authored
421
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
422 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
423 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
424 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
425 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
426 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
427
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
428 The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
429 in Release 1.57 (with the intention of reusing this name space for a GFF
430 parser).
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
431
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
432 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
433 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
434 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
435 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
436
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
437 Bio.SVM
438 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
439 Deprecated as of Release 1.30, removed in Release 1.42.
723313c @cbrueffer Assorted fixes for typos, duplicate words etc.
cbrueffer authored
440 The Support Vector Machine code in Biopython has been superseded by a
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
441 more robust (and maintained) SVM library, which includes a python
442 interface. We recommend using LIBSVM:
443
444 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
445
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
446 Bio.RecordFile
447 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
448 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
449 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
450
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
451 Bio.kMeans and Bio.xkMeans
452 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
453 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
454 the function kcluster in Bio.Cluster which performs k-means or k-medians
455 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
456
457 Bio.InterPro
458 ============
459 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
460 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
461
462 Bio.SCOP
463 ========
464 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
465 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
466 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
467
468 Bio.utils
469 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
470 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
471 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
472 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
473 The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
474 Release 1.56, and removed in Release 1.57.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
475
476 Bio.Motif
477 =========
478 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
479 declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
480 in Release 1.57.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
481 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
482 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
483 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
484 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
485 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
486 deprecated in Release 1.55 final; their functionality is now available through
487 a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
488 respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace Recor…
mdehoon authored
489
490 Bio.Compass
491 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
492 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
c4d0fa8 @peterjc Remove deprecated bits of Bio.Compass
peterjc authored
493 deprecated in Release 1.55, removed in Release 1.59. Their functionality is
494 now available through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
495
496 Bio.Affy.CelFile
497 ================
498 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
9dfbc94 @peterjc Remove deprecated bits of Bio.Affy.CelFile
peterjc authored
499 in Release 1.54, deprecated in Release 1.55 and removed in Release 1.59.
500 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
501
502 Bio.PopGen.FDist
503 ================
504 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
3704a68 @peterjc Update NEWS and DEPRECATED files
peterjc authored
505 in Release 1.54, deprecated in Release 1.55, and removed in Release 1.58.
506 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
507
508 Bio.UniGene
509 ===========
510 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
511 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
512 Bio.UniGene were declared obsolete in Release 1.54, deprecated in Release 1.55,
ecdde52 @peterjc Correct typo in last commit
peterjc authored
513 and removed in Release 1.59. Their functionality is now available through a
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
514 read() and a parse() function in Bio.UniGene.
1b2025b Upgrading obsolete code to deprecated code
Michiel de Hoon authored
515 The HTML parser in Bio.UniGene.UniGene was declared obsolete in Release 1.59,
516 and deprecated in Release 1.61.
815d64f making the obsolete classes more explicit
mdehoon authored
517
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
518 Bio.SubsMat
519 ===========
520 The methods letter_sum and all_letters_sum were removed from the SeqMat class in
521 Bio.SubsMat in Release 1.57.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
522
523 Bio.Align
524 =========
525 The methods get_column and add_sequence of the MultipleSeqAlignment class were
526 deprecated in Release 1.57. The Alignment class in Bio.Align.Generic and its
527 method get_seq_by_num were deprecated in Release 1.57.
c13d64d Updating comments and DEPRECATED file
Michiel de Hoon authored
528
529 Bio.ParserSupport
530 =================
531 Bio.ParserSupport was declared obsolete in Release 1.59.
084c898 @peterjc Remove deprecated Bio.File.StringHandle and SGMLStripper
peterjc authored
532
533 Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59, and
534 removed in Release 1.61.
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