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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
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
10 Bio.Clustalw
11 ============
12 Declared obsolete in Release 1.52, having been replaced with Bio.AlignIO for
13 parsing and writing clustal format alignments (since Release 1.46), and
14 Bio.Align.Applications for calling the ClustalW command line tool (Release
15 1.51). See the Tutorial for examples.
16
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
17 BioSQL and psycopg
18 ==================
19 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
20 in Release 1.51, please use psycopg2 instead.
21
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
22 Bio.Application.generic_run and ApplicationResult
23 =================================================
24 Declared obsolete in Release 1.51, please use Python subprocess module instead.
25
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
26 Bio.Entrez.efetch and rettype="genbank"
27 =======================================
28 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
29 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
30 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
31 automatically, but issues a deprecation warning.
32
33 Bio.Entrez.query function
34 =========================
35 Deprecated in Release 1.47, removed in 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
36
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
37 Bio.SwissProt.SProt
38 ===================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
39 Declared obsolete in Release 1.50, and deprecated in Release 1.51. Most of the
40 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
41
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
42 Bio.Prosite and Bio.Enzyme
43 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
44 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
45 Most of the functionality has moved to Bio.ExPASy.Prosite and
46 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
47
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
48 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
49 =====================================================================
bc953fa @peterjc Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio…
peterjc authored
50 Declared obsolete in Release 1.50, deprecated in Release 1.52.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
51
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
52 Bio.Graphics.GenomeDiagram and colour/color, centre/center
53 ==========================================================
54 GenomeDiagram originally used colour and centre (UK spelling of color and
55 center) for argument names. As part of its integration into Biopython 1.50,
56 this will support both colour and color, and both centre and center, to help
57 people port existing scripts written for the standalone version of
58 GenomeDiagram. However, we do intend to deprecate and then eventually
59 remove support for colour and centre in later releases of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
60
61 Bio.AlignAce and Bio.MEME
62 =========================
e62220a @peterjc Deprecation warnings for Bio.AlignAce and Bio.MEME
peterjc authored
63 Declared obsolete in Release 1.50, and deprecated in Release 1.52. Please
64 use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
65
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
66 Numeric support
67 ===============
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
68 Following the release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
69 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
70
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
71 Bio.Seq and the data property
72 =============================
73 Direct use of the Seq object (and MutableSeq object) .data property is
74 discouraged. As of release 1.49, writing to the Seq object's .data property
75 triggers a warning, and this property is likely to be made read only in the
76 next release.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warnin…
peterjc authored
77
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
78 Bio.Transcribe and Bio.Translate
79 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
80 Declared obsolete in Release 1.49, deprecated in Release 1.51.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
81 Please use the methods or functions in Bio.Seq instead.
82
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
83 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
84 ==========================================
85 Declared obsolete in Release 1.49.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
86 Bio.mathfns and Bio.stringfns were deprecated in Release 1.50
87 (the deprecation of Bio.listfns is still pending)
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
88
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
89 Bio.distance (and Bio.cdistance)
90 ================================
91 Bio.distance was deprecated in Release 1.49, at which point its C code
92 implementation Bio.cdistance was removed (this was not intended as a public
93 API).
94
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
95 Bio.Ndb
96 =======
97 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
98 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
99
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
100 Martel
101 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
102 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
103 in Release 1.51. The source code for Martel is still in our repository if
104 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
105
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
106 Bio.Mindy and associated modules.
107 =================================
108 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
109 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
110 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
111
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
112 Bio.Fasta index_file and Dictionary
113 ===================================
114 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
115 sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of
8af957d @peterjc Adding the Bio.SeqIO.indexed_dict() function developed on a github br…
peterjc authored
116 SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.indexed_dict()
117 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
118
119 Bio.Fasta (including Bio.Fasta.FastaAlign)
120 ==========================================
121 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
122 Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
123
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
124 Bio.Align.FormatConvert
125 =======================
126 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
127 Please use Bio.AlignIO or the Alignment object's format method instead.
128
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
129 Bio.Emboss.Primer
130 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
131 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
132 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
133
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
134 Bio.MetaTool
135 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
136 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
137 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
138
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
139 Bio.GenBank
140 ===========
141 The online functionality (search_for, download_many, and NCBIDictionary) was
5b78a4e @peterjc Deprecating the online bits of Bio.GenBank in favour of Bio.Entrez (t…
peterjc authored
142 declared obsolete in Release 1.48, and deprecated in Release 1.50.
143 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
144
145 Bio.PubMed
146 ==========
558b4c0 @peterjc Deprecating Bio.PubMed in favour of Bio.Entrez
peterjc authored
147 Declared obsolete in Release 1.48, deprecated in Release 1.49.
148 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
149
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
150 Bio.EUtils
151 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
152 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
153
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
154 Bio.Sequencing & Bio.Medline
155 ============================
156 A revised API was added and the old one deprecated in Release 1.48,
157 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
158 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
159 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
160 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
161 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
162 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
163 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
164
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
165 Bio.Blast.NCBIWWW
166 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
167 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
168 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
169
170 Bio.Saf
171 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
172 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
173 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
174
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
175 Bio.NBRF
176 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
177 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
178 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
179
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
180 Bio.IntelliGenetics
181 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
182 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
183 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
184
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
185 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
186 =================================================================
187 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
188 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
189 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
190
5e507c9 Updating for release 1.47.
mdehoon authored
191 Bio.ECell
192 =========
193 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
194 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
195
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
196 Bio.Ais
197 =======
198 Deprecated as of Release 1.45, removed in Release 1.49.
199
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
200 Bio.LocusLink
201 =============
202 Deprecated as of Release 1.45, removed in Release 1.49.
203 The NCBI's LocusLink was superseded by Entrez Gene.
204
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
205 Bio.SGMLExtractor
206 =================
207 Deprecated as of Release 1.46, removed in Release 1.49.
208
d01c450 Getting ready for release 1.46.
mdehoon authored
209 Bio.Rebase
210 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
211 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
212
213 Bio.Gobase
214 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
215 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
216
217 Bio.CDD
218 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
219 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
220
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
221 Bio.biblio
222 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
223 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
224
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
225 Bio.WWW
226 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
227 The modules under Bio.WWW were deprecated in Release 1.45, and removed in
228 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
229
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
230 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
231 is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
232
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
233 Bio.SeqIO
234 =========
235 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
236 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
237
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
238 Bio.Medline.NLMMedlineXML
239 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
240 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
241
242 Bio.MultiProc
243 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
244 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
245
246 Bio.MarkupEditor
247 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
248 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
249
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
250 Bio.lcc
251 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
252 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
253
254 Bio.crc
255 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
256 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
257
258 Bio.FormatIO
259 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
260 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
261
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
262 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
263 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
264 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
265
266 Bio.Kabat
267 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
268 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
269
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
270 Bio.SeqUtils
271 ============
272 The functions 'complement' and 'antiparallel' in Bio.SeqUtils have been
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
273 deprecated as of Release 1.31, and removed in Release 1.43.
274 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
275
276 Bio.GFF
277 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
278 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
279 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
280 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
281
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
282 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
283 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
284 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
285 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
286
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
287 Bio.SVM
288 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
289 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
290 The Support Vector Machine code in Biopython has been superceeded by a
291 more robust (and maintained) SVM library, which includes a python
292 interface. We recommend using LIBSVM:
293
294 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
295
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
296 Bio.RecordFile
297 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
298 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
299 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
300
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
301 Bio.kMeans and Bio.xkMeans
302 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
303 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
304 the function kcluster in Bio.Cluster which performs k-means or k-medians
305 clustering.
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