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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 ==========
12 As of Biopython 1.54, we consider support for Python 2.4 to be deprecated.
13 This means we will continue to support Python 2.4 for at least two further
14 releases, and at least one year (whichever takes longer), before dropping
15 support for Python 2.4. This can be delayed given feedback from our users
16 (e.g. if this proves to be a problem in combination with other libraries).
17
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprec…
peterjc authored
18 Bio.Restriction.DNAUtils and check_bases
19 ========================================
20 This module (originally in C) offered complement and antiparallel functions
21 (duplicating functionality in Bio.Seq) and a rather odd function called
22 check_bases (also available as Bio.Restriction.Restriction.check_bases).
23 Deprecated in Release 1.53.
24
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
25 Bio.Blast.NCBIStandalone
26 ========================
27 The three functions for calling the "legacy" NCBI BLAST command line tools
28 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
29 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications and the Python
30 subprocess module instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
31
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailin…
peterjc authored
32 The remainder of this module is a parser for the plain text BLAST output,
33 which was delclared obsolete in Release 1.54. For some time now, both the NCBI
34 and Biopython have encouraged people to parse the XML output instead.
35
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
36 Bio.Blast.Applications
37 ======================
38 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
39 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
40 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g.
41 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as o…
peterjc authored
42
cbb051b @peterjc Note about the old EMBOSS PHYLIP wrappers being obsolete
peterjc authored
43 Bio.EMBOSS.Applications
44 =======================
45 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
46 obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS
47 PHYLIP tools (e.g. fneighbor) instead.
48
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest exam…
peterjc authored
49 Bio.Clustalw
50 ============
51 Declared obsolete in Release 1.52, having been replaced with Bio.AlignIO for
52 parsing and writing clustal format alignments (since Release 1.46), and
53 Bio.Align.Applications for calling the ClustalW command line tool (Release
54 1.51). See the Tutorial for examples.
55
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
56 BioSQL and psycopg
57 ==================
58 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
59 in Release 1.51, please use psycopg2 instead.
60
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
61 Bio.Application.generic_run and ApplicationResult
62 =================================================
2c7126b @peterjc Updating DEPRECATED file regarding Bio.Application and Bio.WWW
peterjc authored
63 Declared obsolete in Release 1.51, and deprecated in Release 1.53.
64 Please use the Python subprocess module instead.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
65
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
66 Bio.Entrez.efetch and rettype="genbank"
67 =======================================
68 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
69 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
70 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
71 automatically, but issues a deprecation warning.
72
73 Bio.Entrez.query function
74 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obs…
peterjc authored
75 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
76
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
77 Bio.SwissProt.SProt
78 ===================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
79 Declared obsolete in Release 1.50, and deprecated in Release 1.51. Most of the
80 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
81
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
82 Bio.Prosite and Bio.Enzyme
83 ==========================
7b2a1a5 @peterjc Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc authored
84 Declared obsolete in Release 1.50, and deprecated in Release 1.53.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
85 Most of the functionality has moved to Bio.ExPASy.Prosite and
86 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
87
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
88 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
89 =====================================================================
bc953fa @peterjc Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle and Bio…
peterjc authored
90 Declared obsolete in Release 1.50, deprecated in Release 1.52.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
91
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
92 Bio.Graphics.GenomeDiagram and colour/color, centre/center
93 ==========================================================
94 GenomeDiagram originally used colour and centre (UK spelling of color and
95 center) for argument names. As part of its integration into Biopython 1.50,
96 this will support both colour and color, and both centre and center, to help
97 people port existing scripts written for the standalone version of
98 GenomeDiagram. However, we do intend to deprecate and then eventually
99 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
100
101 Bio.AlignAce and Bio.MEME
102 =========================
e62220a @peterjc Deprecation warnings for Bio.AlignAce and Bio.MEME
peterjc authored
103 Declared obsolete in Release 1.50, and deprecated in Release 1.52. Please
104 use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
105
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
106 Numeric support
107 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
108 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
109 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
110
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
111 Bio.Seq and the data property
112 =============================
113 Direct use of the Seq object (and MutableSeq object) .data property is
362d4c5 @peterjc Making Seq.data read only
peterjc authored
114 discouraged. As of Release 1.49, writing to the Seq object's .data property
115 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 warnin…
peterjc authored
116
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
117 Bio.Transcribe and Bio.Translate
118 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
119 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
120 Please use the methods or functions in Bio.Seq instead.
121
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
122 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
123 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and…
peterjc authored
124 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
125 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
126 The three C implementations were all removed in Release 1.53. Bio.mathfns
127 and Bio.stringfns were removed in Release 1.55.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
128
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
129 Bio.distance (and Bio.cdistance)
130 ================================
131 Bio.distance was deprecated in Release 1.49, at which point its C code
132 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
133 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
134
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
135 Bio.Ndb
136 =======
137 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
138 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
139
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
140 Martel
141 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
142 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
143 in Release 1.51. The source code for Martel is still in our repository if
144 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
145
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
146 Bio.Mindy and associated modules.
147 =================================
148 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
149 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
150 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
151
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
152 Bio.Fasta index_file and Dictionary
153 ===================================
154 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
155 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
156 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
157 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
158
159 Bio.Fasta (including Bio.Fasta.FastaAlign)
160 ==========================================
161 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
162 Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
163
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
164 Bio.Align.FormatConvert
165 =======================
166 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
167 Please use Bio.AlignIO or the Alignment object's format method instead.
168
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
169 Bio.Emboss.Primer
170 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Mar…
peterjc authored
171 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
172 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
173
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
174 Bio.MetaTool
175 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
176 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
177 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
178
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
179 Bio.GenBank
180 ===========
181 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
182 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
183 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
184
185 Bio.PubMed
186 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
187 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
188 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
189
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
190 Bio.EUtils
191 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
192 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
193
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
194 Bio.Sequencing & Bio.Medline
195 ============================
196 A revised API was added and the old one deprecated in Release 1.48,
197 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
198 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
199 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
200 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
201 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
202 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
203 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
204
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
205 Bio.Blast.NCBIWWW
206 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
207 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
208 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
209
210 Bio.Saf
211 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
212 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
213 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
214
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
215 Bio.NBRF
216 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
217 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
218 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
219
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
220 Bio.IntelliGenetics
221 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
222 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
223 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
224
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
225 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
226 =================================================================
227 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
228 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
229 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
230
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
231 Bio.SeqIO.to_alignment()
232 ========================
233 This function was made obsolete with the introduction of Bio.AlignIO,
234 and deprecated in Release 1.54. Use either the Bio.AlignIO functions,
235 or the Bio.Align.MultipleSeqAlignment class directly instead.
236
5e507c9 Updating for release 1.47.
mdehoon authored
237 Bio.ECell
238 =========
239 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
240 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
241
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
242 Bio.Ais
243 =======
244 Deprecated as of Release 1.45, removed in Release 1.49.
245
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
246 Bio.LocusLink
247 =============
248 Deprecated as of Release 1.45, removed in Release 1.49.
249 The NCBI's LocusLink was superseded by Entrez Gene.
250
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
251 Bio.SGMLExtractor
252 =================
253 Deprecated as of Release 1.46, removed in Release 1.49.
254
d01c450 Getting ready for release 1.46.
mdehoon authored
255 Bio.Rebase
256 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
257 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
258
259 Bio.Gobase
260 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
261 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
262
263 Bio.CDD
264 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
265 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
266
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
267 Bio.biblio
268 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
269 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
270
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
271 Bio.WWW
272 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
273 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
274 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
275 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
276
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bi…
peterjc authored
277 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
278 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
279 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
280
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
281 Bio.SeqIO
282 =========
283 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
284 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
285
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
286 Bio.Medline.NLMMedlineXML
287 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
288 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
289
290 Bio.MultiProc
291 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
292 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
293
294 Bio.MarkupEditor
295 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
296 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
297
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
298 Bio.lcc
299 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
300 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
301
302 Bio.crc
303 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
304 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
305
306 Bio.FormatIO
307 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
308 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
309
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
310 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
311 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
312 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
313
314 Bio.Kabat
315 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
316 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
317
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
318 Bio.SeqUtils
319 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
320 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
321 in Release 1.31, and removed in Release 1.43. Function 'translate' was
322 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
323 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
324
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…
peterjc authored
325 Function makeTableX and classes ProteinX and MissingTable were deprecated
326 in Release 1.54. These were remnants of the removed translate function,
327 and no longer served any useful purpose.
328
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
329 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
330 just use the string's slice method with a step of minus one.
331
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
332 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
333 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
334 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
335 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
336 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
337
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
338 The whole of the old Bio.GFF module was deprecated in Release 1.53
339 (with the intention of reusing this name space for a GFF parser).
340
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
341 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
342 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
343 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
344 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
345
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
346 Bio.SVM
347 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
348 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
349 The Support Vector Machine code in Biopython has been superceeded by a
350 more robust (and maintained) SVM library, which includes a python
351 interface. We recommend using LIBSVM:
352
353 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
354
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
355 Bio.RecordFile
356 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
357 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
358 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
359
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
360 Bio.kMeans and Bio.xkMeans
361 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
362 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
363 the function kcluster in Bio.Cluster which performs k-means or k-medians
364 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
365
366 Bio.InterPro
367 ============
368 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
369 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
370
371 Bio.SCOP
372 ========
373 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
374 Release 1.53.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
375
376 Bio.utils
377 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in …
peterjc authored
378 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_t…
mdehoon authored
379 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
380 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
381
382 Bio.Motif
383 =========
384 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
40ff78e Updating the DEPRECATED file concerning the parser simplifications in…
mdehoon authored
385 deprecated in Release 1.53. AlignAceConsumer, AlignAceParser, and
386 AlignAceScanner were declared obsolete in Release 1.53; their functionality is
387 now available through a read() function in Bio.Motif.Parsers.AlignAce.
815d64f making the obsolete classes more explicit
mdehoon authored
388 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
389 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54; their
390 functionality is now available through a read() function in
391 Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST, respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace Recor…
mdehoon authored
392
393 Bio.Compass
394 ===========
395 The RecordParser and Iterator classes were declared obsolete in Release 1.54.
396 Their functionality is now available through a read() and a parse() function,
397 respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
398
399 Bio.Affy.CelFile
400 ================
401 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
402 in Release 1.54. Their functionality is now available through a read()
403 function.
404
405 Bio.PopGen.FDist
406 ================
407 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
408 in Release 1.54. Their functionality is now available through a read() function.
409
410 Bio.UniGene
411 ===========
412 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
413 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
414 Bio.UniGene were declared obsolete in Release 1.54. Their functionality is now
415 available through a read() and a parse() function in Bio.UniGene.
416
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