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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
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
5 Bio.Prosite and Bio.Enzyme
6 ==========================
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
7 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
8 Most of the functionality has moved to Bio.ExPASy.Prosite and
9 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
10
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bio.F...
peterjc authored
11 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
12 =====================================================================
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
13 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
14
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
15 Bio.Graphics.GenomeDiagram and colour/color, centre/center
16 ==========================================================
17 GenomeDiagram originally used colour and centre (UK spelling of color and
18 center) for argument names. As part of its integration into Biopython 1.50,
19 this will support both colour and color, and both centre and center, to help
20 people port existing scripts written for the standalone version of
21 GenomeDiagram. However, we do intend to deprecate and then eventually
22 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
23
24 Bio.AlignAce and Bio.MEME
25 =========================
26 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 Bio...
peterjc authored
27 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 chan...
peterjc authored
28
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
29 Numeric support
30 ===============
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
31 Following the release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
32 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
33
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
34 Bio.Seq and the data property
35 =============================
36 Direct use of the Seq object (and MutableSeq object) .data property is
37 discouraged. As of release 1.49, writing to the Seq object's .data property
38 triggers a warning, and this property is likely to be made read only in the
39 next release.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warning w...
peterjc authored
40
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
41 Bio.Transcribe and Bio.Translate
42 ================================
43 Declared obsolete in Release 1.49.
44 Please use the methods or functions in Bio.Seq instead.
45
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
46 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
47 ==========================================
48 Declared obsolete in Release 1.49.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
49 Bio.mathfns and Bio.stringfns were deprecated in Release 1.50
50 (the deprecation of Bio.listfns is still pending)
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
51
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
52 Bio.distance (and Bio.cdistance)
53 ================================
54 Bio.distance was deprecated in Release 1.49, at which point its C code
55 implementation Bio.cdistance was removed (this was not intended as a public
56 API).
57
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
58 Bio.Ndb
59 =======
60 Deprecated in Release 1.49, as the website this parsed has been redesigned.
61
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
62 Martel
63 ======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
64 Declared obsolete in Release 1.48, deprecated in Release 1.49.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
65
66 Bio.Mindy
67 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
68 Declared obsolete in Release 1.48, deprecated in Release 1.49.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
69
1b6c598 @peterjc Deprecating Bio.DBXRef which was used in the Bio.builders Martel parsing...
peterjc authored
70 Bio.builders, Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef
71 ================================================================
72 Part of the Martel/Mindy parsing infrastructure, these were deprecated in
73 Release 1.49.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
74
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.writ...
peterjc authored
75 Bio.Writer and Bio.writers
76 ==========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
77 Deprecated in Release 1.48.
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.writ...
peterjc authored
78
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
79 Bio.Emboss.Primer
80 =================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
81 Deprecated in Release 1.48, this parser was replaced by Bio.Emboss.Primer3
82 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
83
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
84 Bio.MetaTool
85 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
86 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 this...
peterjc authored
87 which is now obsolete.
88
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
89 Bio.GenBank
90 ===========
91 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
92 declared obsolete in Release 1.48, and deprecated in Release 1.50.
93 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
94
95 Bio.PubMed
96 ==========
558b4c0 @peterjc Deprecating Bio.PubMed in favour of Bio.Entrez
peterjc authored
97 Declared obsolete in Release 1.48, deprecated in Release 1.49.
98 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
99
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
100 Bio.EUtils
101 ==========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
102 Deprecated in favor of Bio.Entrez in Release 1.48.
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
103
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
104 Bio.Sequencing
105 ==============
106 A revised API was added and the old one deprecated in Biopython 1.48:
107 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
108 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
109 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
110 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
111
112
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
113 Bio.Blast.NCBIWWW
114 =================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
115 The HTML BLAST parser was deprecated as of Release 1.48.
116 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
117
118 Bio.Saf
119 =======
120 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 mi...
peterjc authored
121 on Martel which doesn't work properly with mxTextTools 3.0.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
122
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
123 Bio.NBRF
124 ========
125 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO
126
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
127 Bio.IntelliGenetics
128 ===================
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
129 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO
d01c450 Getting ready for release 1.46.
mdehoon authored
130
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
131 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
132 =================================================================
133 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
134 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
135 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
136
5e507c9 Updating for release 1.47.
mdehoon authored
137 Bio.ECell
138 =========
139 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
140 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
141
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
142 Bio.Ais
143 =======
144 Deprecated as of Release 1.45, removed in Release 1.49.
145
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
146 Bio.LocusLink
147 =============
148 Deprecated as of Release 1.45, removed in Release 1.49.
149 The NCBI's LocusLink was superseded by Entrez Gene.
150
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
151 Bio.SGMLExtractor
152 =================
153 Deprecated as of Release 1.46, removed in Release 1.49.
154
d01c450 Getting ready for release 1.46.
mdehoon authored
155 Bio.Rebase
156 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
157 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
158
159 Bio.Gobase
160 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
161 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
162
163 Bio.CDD
164 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
165 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
166
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
167 Bio.biblio
168 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
169 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
170
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
171 Bio.WWW
172 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
173 The modules under Bio.WWW were deprecated in Release 1.45, and removed in
174 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 remo...
peterjc authored
175
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
176 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
177 is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
178
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
179 Bio.SeqIO
180 =========
181 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
182 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
183
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
184 Bio.Medline.NLMMedlineXML
185 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
186 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
187
188 Bio.MultiProc
189 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
190 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
191
192 Bio.MarkupEditor
193 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
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
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
196 Bio.lcc
197 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
198 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
199
200 Bio.crc
201 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
202 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
203
204 Bio.FormatIO
205 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
206 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
207
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
208 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
209 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
210 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
211
212 Bio.Kabat
213 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
214 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
215
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
216 Bio.SeqUtils
217 ============
218 The functions 'complement' and 'antiparallel' in Bio.SeqUtils have been
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
219 deprecated as of Release 1.31, and removed in Release 1.43.
220 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
221
222 Bio.GFF
223 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
224 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
225 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
226 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
227
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
228 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
229 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
230 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
231 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
232
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
233 Bio.SVM
234 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
235 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
236 The Support Vector Machine code in Biopython has been superceeded by a
237 more robust (and maintained) SVM library, which includes a python
238 interface. We recommend using LIBSVM:
239
240 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
241
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
242 Bio.RecordFile
243 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
244 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
245 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
246
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
247 Bio.kMeans and Bio.xkMeans
248 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
249 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
250 the function kcluster in Bio.Cluster which performs k-means or k-medians
251 clustering.
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