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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
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
10 Bio.Restriction.DNAUtils and check_bases
11 ========================================
12 This module (originally in C) offered complement and antiparallel functions
13 (duplicating functionality in Bio.Seq) and a rather odd function called
14 check_bases (also available as Bio.Restriction.Restriction.check_bases).
15 Deprecated in Release 1.53.
16
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
17 Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast
18 ========================================================
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
19 These command line tools calling functions were declared obsolete in Release
20 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications and the Python
21 subprocess module instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
22
23 Bio.Blast.Applications
24 ======================
25 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
26 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
27 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
28 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
29
cbb051b @peterjc Note about the old EMBOSS PHYLIP wrappers being obsolete
peterjc authored
30 Bio.EMBOSS.Applications
31 =======================
32 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
33 obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
34 PHYLIP tools (e.g. fneighbor) instead.
35
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
36 Bio.Clustalw
37 ============
38 Declared obsolete in Release 1.52, having been replaced with Bio.AlignIO for
39 parsing and writing clustal format alignments (since Release 1.46), and
40 Bio.Align.Applications for calling the ClustalW command line tool (Release
41 1.51). See the Tutorial for examples.
42
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
43 BioSQL and psycopg
44 ==================
45 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
46 in Release 1.51, please use psycopg2 instead.
47
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
48 Bio.Application.generic_run and ApplicationResult
49 =================================================
2c7126b @peterjc Updating DEPRECATED file regarding Bio.Application and Bio.WWW
peterjc authored
50 Declared obsolete in Release 1.51, and deprecated in Release 1.53.
51 Please use the Python subprocess module instead.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
52
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
53 Bio.Entrez.efetch and rettype="genbank"
54 =======================================
55 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
56 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
57 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
58 automatically, but issues a deprecation warning.
59
60 Bio.Entrez.query function
61 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
62 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
63
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
64 Bio.SwissProt.SProt
65 ===================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
66 Declared obsolete in Release 1.50, and deprecated in Release 1.51. Most of the
67 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
68
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
69 Bio.Prosite and Bio.Enzyme
70 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
71 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
72 Most of the functionality has moved to Bio.ExPASy.Prosite and
73 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
74
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bio.F...
peterjc authored
75 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
76 =====================================================================
bc953fa @peterjc Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio.Fi...
peterjc authored
77 Declared obsolete in Release 1.50, deprecated in Release 1.52.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
78
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
79 Bio.Graphics.GenomeDiagram and colour/color, centre/center
80 ==========================================================
81 GenomeDiagram originally used colour and centre (UK spelling of color and
82 center) for argument names. As part of its integration into Biopython 1.50,
83 this will support both colour and color, and both centre and center, to help
84 people port existing scripts written for the standalone version of
85 GenomeDiagram. However, we do intend to deprecate and then eventually
86 remove support for colour and centre in later releases of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
87
88 Bio.AlignAce and Bio.MEME
89 =========================
e62220a @peterjc Deprecation warnings for Bio.AlignAce and Bio.MEME
peterjc authored
90 Declared obsolete in Release 1.50, and deprecated in Release 1.52. Please
91 use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
92
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
93 Numeric support
94 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
95 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
96 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
97
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
98 Bio.Seq and the data property
99 =============================
100 Direct use of the Seq object (and MutableSeq object) .data property is
362d4c5 @peterjc Making Seq.data read only
peterjc authored
101 discouraged. As of Release 1.49, writing to the Seq object's .data property
102 triggered a warning, and this property was made read only in Release 1.53.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warning w...
peterjc authored
103
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
104 Bio.Transcribe and Bio.Translate
105 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obsolet...
peterjc authored
106 Declared obsolete in Release 1.49, deprecated in Release 1.51.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
107 Please use the methods or functions in Bio.Seq instead.
108
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
109 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
110 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and st...
peterjc authored
111 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
112 deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53.
113 The three C implementations were all removed in Release 1.53.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
114
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
115 Bio.distance (and Bio.cdistance)
116 ================================
117 Bio.distance was deprecated in Release 1.49, at which point its C code
118 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
119 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
120
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
121 Bio.Ndb
122 =======
123 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
124 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
125
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
126 Martel
127 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
128 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
129 in Release 1.51. The source code for Martel is still in our repository if
130 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
131
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
132 Bio.Mindy and associated modules.
133 =================================
134 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
135 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
136 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
137
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
138 Bio.Fasta index_file and Dictionary
139 ===================================
140 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
141 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
142 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
143 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
144
145 Bio.Fasta (including Bio.Fasta.FastaAlign)
146 ==========================================
147 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
148 Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
149
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
150 Bio.Align.FormatConvert
151 =======================
152 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
153 Please use Bio.AlignIO or the Alignment object's format method instead.
154
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
155 Bio.Emboss.Primer
156 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Martel...
peterjc authored
157 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
158 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
159
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
160 Bio.MetaTool
161 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
162 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
163 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
164
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
165 Bio.GenBank
166 ===========
167 The online functionality (search_for, download_many, and NCBIDictionary) was
5b78a4e @peterjc Deprecating the online bits of Bio.GenBank in favour of Bio.Entrez (thes...
peterjc authored
168 declared obsolete in Release 1.48, and deprecated in Release 1.50.
169 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
170
171 Bio.PubMed
172 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
173 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
174 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
175
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
176 Bio.EUtils
177 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
178 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
179
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
180 Bio.Sequencing & Bio.Medline
181 ============================
182 A revised API was added and the old one deprecated in Release 1.48,
183 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
184 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
185 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
186 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
187 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
188 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
189 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
190
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
191 Bio.Blast.NCBIWWW
192 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
193 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
194 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
195
196 Bio.Saf
197 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
198 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
199 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
200
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
201 Bio.NBRF
202 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
203 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
204 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
205
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
206 Bio.IntelliGenetics
207 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
208 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
209 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
210
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
211 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
212 =================================================================
213 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
214 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
215 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
216
5e507c9 Updating for release 1.47.
mdehoon authored
217 Bio.ECell
218 =========
219 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
220 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
221
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
222 Bio.Ais
223 =======
224 Deprecated as of Release 1.45, removed in Release 1.49.
225
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
226 Bio.LocusLink
227 =============
228 Deprecated as of Release 1.45, removed in Release 1.49.
229 The NCBI's LocusLink was superseded by Entrez Gene.
230
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
231 Bio.SGMLExtractor
232 =================
233 Deprecated as of Release 1.46, removed in Release 1.49.
234
d01c450 Getting ready for release 1.46.
mdehoon authored
235 Bio.Rebase
236 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
237 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
238
239 Bio.Gobase
240 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
241 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
242
243 Bio.CDD
244 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
245 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
246
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
247 Bio.biblio
248 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
249 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
250
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
251 Bio.WWW
252 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
253 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
254 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
255 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
256
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
257 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
258 is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
259
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
260 Bio.SeqIO
261 =========
262 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
263 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
264
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
265 Bio.Medline.NLMMedlineXML
266 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
267 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
268
269 Bio.MultiProc
270 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
271 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
272
273 Bio.MarkupEditor
274 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
275 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
276
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
277 Bio.lcc
278 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
279 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
280
281 Bio.crc
282 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
283 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
284
285 Bio.FormatIO
286 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
287 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
288
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
289 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
290 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
291 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
292
293 Bio.Kabat
294 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
295 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
296
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
297 Bio.SeqUtils
298 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
299 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
300 in Release 1.31, and removed in Release 1.43. Function 'translate' was
301 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
302 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
303
304 Bio.GFF
305 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
306 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
307 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
308 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
309
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
310 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
311 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
312 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
313 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
314
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
315 Bio.SVM
316 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
317 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
318 The Support Vector Machine code in Biopython has been superceeded by a
319 more robust (and maintained) SVM library, which includes a python
320 interface. We recommend using LIBSVM:
321
322 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
323
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
324 Bio.RecordFile
325 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
326 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
327 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
328
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
329 Bio.kMeans and Bio.xkMeans
330 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
331 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
332 the function kcluster in Bio.Cluster which performs k-means or k-medians
333 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
334
335 Bio.InterPro
336 ============
337 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
338 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
339
340 Bio.SCOP
341 ========
342 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
343 Release 1.53.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
344
345 Bio.utils
346 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
347 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
348 and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
349 1.53. Function 'ungap' was deprecated in Release 1.53.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
350
351 Bio.Motif
352 =========
353 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
354 deprecated in Release 1.53.
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