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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
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
5 Bio.Entrez.efetch and rettype="genbank"
6 =======================================
7 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
8 of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp"
9 (GenPept). Bio.Entrez.efetch will correct this automatically, but issues a
10 deprecation warning.
11
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
12 Bio.SwissProt.SProt
13 ===================
14 Declared obsolete in Release 1.50, and is likely to be deprecated in a future
15 release. Most of the functionality in Bio.SwissProt.SProt is available from
16 Bio.SwissProt. Note that Bio.SeqIO currently still uses Bio.SwissProt.SProt;
17 this will have to be rectified in a future release.
18
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
19 Bio.Prosite and Bio.Enzyme
20 ==========================
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
21 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
22 Most of the functionality has moved to Bio.ExPASy.Prosite and
23 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
24
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
25 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
26 =====================================================================
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
27 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
28
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
29 Bio.Graphics.GenomeDiagram and colour/color, centre/center
30 ==========================================================
31 GenomeDiagram originally used colour and centre (UK spelling of color and
32 center) for argument names. As part of its integration into Biopython 1.50,
33 this will support both colour and color, and both centre and center, to help
34 people port existing scripts written for the standalone version of
35 GenomeDiagram. However, we do intend to deprecate and then eventually
36 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
37
38 Bio.AlignAce and Bio.MEME
39 =========================
40 As of Biopython 1.50, these modules are considered to be obsolete with the
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
41 introduction of Bio.Motif, and they will be deprecated in a future release.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
42
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
43 Numeric support
44 ===============
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
45 Following the release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
46 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
47
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
48 Bio.Seq and the data property
49 =============================
50 Direct use of the Seq object (and MutableSeq object) .data property is
51 discouraged. As of release 1.49, writing to the Seq object's .data property
52 triggers a warning, and this property is likely to be made read only in the
53 next release.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warnin…
peterjc authored
54
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
55 Bio.Transcribe and Bio.Translate
56 ================================
57 Declared obsolete in Release 1.49.
58 Please use the methods or functions in Bio.Seq instead.
59
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
60 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
61 ==========================================
62 Declared obsolete in Release 1.49.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
63 Bio.mathfns and Bio.stringfns were deprecated in Release 1.50
64 (the deprecation of Bio.listfns is still pending)
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
65
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
66 Bio.distance (and Bio.cdistance)
67 ================================
68 Bio.distance was deprecated in Release 1.49, at which point its C code
69 implementation Bio.cdistance was removed (this was not intended as a public
70 API).
71
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
72 Bio.Ndb
73 =======
74 Deprecated in Release 1.49, as the website this parsed has been redesigned.
75
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
76 Martel
77 ======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
78 Declared obsolete in Release 1.48, deprecated in Release 1.49.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
79
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
80 Bio.Mindy and associated modules.
81 =================================
82 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
83 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
84 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
85
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
86 Bio.Emboss.Primer
87 =================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
88 Deprecated in Release 1.48, this parser was replaced by Bio.Emboss.Primer3
89 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
90
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
91 Bio.MetaTool
92 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
93 Deprecated in Release 1.48, this was a parser for the output of MetaTool 3.5
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
94 which is now obsolete.
95
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
96 Bio.GenBank
97 ===========
98 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
99 declared obsolete in Release 1.48, and deprecated in Release 1.50.
100 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
101
102 Bio.PubMed
103 ==========
558b4c0 @peterjc Deprecating Bio.PubMed in favour of Bio.Entrez
peterjc authored
104 Declared obsolete in Release 1.48, deprecated in Release 1.49.
105 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
106
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
107 Bio.EUtils
108 ==========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
109 Deprecated in favor of Bio.Entrez in Release 1.48.
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
110
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
111 Bio.Sequencing
112 ==============
113 A revised API was added and the old one deprecated in Biopython 1.48:
114 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
115 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
116 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
117 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
118
119
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
120 Bio.Blast.NCBIWWW
121 =================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
122 The HTML BLAST parser was deprecated as of Release 1.48.
123 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
124
125 Bio.Saf
126 =======
127 Deprecated as of Release 1.48, as it appears to have no users, and relies
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
128 on Martel which doesn't work properly with mxTextTools 3.0.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
129
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
130 Bio.NBRF
131 ========
132 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO
133
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
134 Bio.IntelliGenetics
135 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
136 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
137 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
138
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
139 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
140 =================================================================
141 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
142 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
143 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
144
5e507c9 Updating for release 1.47.
mdehoon authored
145 Bio.ECell
146 =========
147 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
148 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
149
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
150 Bio.Ais
151 =======
152 Deprecated as of Release 1.45, removed in Release 1.49.
153
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
154 Bio.LocusLink
155 =============
156 Deprecated as of Release 1.45, removed in Release 1.49.
157 The NCBI's LocusLink was superseded by Entrez Gene.
158
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
159 Bio.SGMLExtractor
160 =================
161 Deprecated as of Release 1.46, removed in Release 1.49.
162
d01c450 Getting ready for release 1.46.
mdehoon authored
163 Bio.Rebase
164 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
165 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
166
167 Bio.Gobase
168 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
169 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
170
171 Bio.CDD
172 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
173 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
174
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
175 Bio.biblio
176 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
177 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
178
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
179 Bio.WWW
180 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
181 The modules under Bio.WWW were deprecated in Release 1.45, and removed in
182 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
183
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
184 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
185 is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
186
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
187 Bio.SeqIO
188 =========
189 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
190 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
191
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
192 Bio.Medline.NLMMedlineXML
193 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
194 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
195
196 Bio.MultiProc
197 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
198 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
199
200 Bio.MarkupEditor
201 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
202 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
203
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
204 Bio.lcc
205 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
206 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
207
208 Bio.crc
209 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
210 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
211
212 Bio.FormatIO
213 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
214 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
215
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
216 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
217 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
218 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
219
220 Bio.Kabat
221 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
222 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
223
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
224 Bio.SeqUtils
225 ============
226 The functions 'complement' and 'antiparallel' in Bio.SeqUtils have been
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
227 deprecated as of Release 1.31, and removed in Release 1.43.
228 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
229
230 Bio.GFF
231 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
232 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
233 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
234 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
235
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
236 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
237 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
238 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
239 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
240
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
241 Bio.SVM
242 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
243 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
244 The Support Vector Machine code in Biopython has been superceeded by a
245 more robust (and maintained) SVM library, which includes a python
246 interface. We recommend using LIBSVM:
247
248 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
249
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
250 Bio.RecordFile
251 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
252 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
253 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
254
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
255 Bio.kMeans and Bio.xkMeans
256 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
257 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
258 the function kcluster in Bio.Cluster which performs k-means or k-medians
259 clustering.
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