Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Newer
Older
100644 487 lines (400 sloc) 18.831 kb
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
1 This file provides documentation for modules in Biopython that have been moved
2 or deprecated in favor of other modules. This provides some quick and easy
3 to find documentation about how to update your code to work again.
4
b4379ed @peterjc Dropping support for Python 2.3
peterjc authored
5 Python 2.3
6 ==========
7 No longer supported as of Release 1.51, having triggered a warning with
8 Release 1.50, with a mention in the release notes for Release 1.49.
9
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
10 Python 2.4
11 ==========
9cdfacb @peterjc Clarify Python 2.4 status in DEPRECATED file
peterjc authored
12 No longer supported as of Release 1.59, having triggered a warning since
13 Release 1.55, with advance notice in the release notes for Release 1.54.
37eec9c @peterjc Adding note about phasing out support for Python 2.4
peterjc authored
14
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
15 Bio.Encodings
16 =============
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
17 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
18 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
19
20 Bio.PropertyManager
21 ===================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
22 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
23 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
24
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
25 Bio.InterPro
26 ============
4749068 @peterjc Remove deprecated Bio.InterPro module (HTML parser)
peterjc authored
27 This module was a parser for the EBI InterPro webpages, but no longer worked
28 with their current website. Deprecated in Release 1.55, and removed in
29 Release 1.58.
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
30
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
31 Bio.GenBank.LocationParser
32 ==========================
33 This module used to be used for parsing GenBank and EMBL feature locations.
34 It has been replaced with faster code using regular expressions, and is no
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.spar...
peterjc authored
35 longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
36
37 Bio.Parsers and Bio.Parsers.spark
38 =================================
39 This module was a copy of John Aycock's SPARK parser included with Biopython
f38249a @peterjc Fixed a typo
peterjc authored
40 soley for use in Bio.GenBank.LocationParser. Declared obsolete in Release
d6caa36 @peterjc Deprecating Bio.GenBank.LocationParser, Bio.Parsers and Bio.Parsers.spar...
peterjc authored
41 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
42
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
43 Bio.Restriction.DNAUtils and check_bases
44 ========================================
45 This module (originally in C) offered complement and antiparallel functions
46 (duplicating functionality in Bio.Seq) and a rather odd function called
47 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
48 Deprecated in Release 1.53, removed in Release 1.57.
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
49
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
50 Bio.Blast.NCBIStandalone
51 ========================
52 The three functions for calling the "legacy" NCBI BLAST command line tools
53 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ad5ea06 @peterjc Clarify DEPRECATED file regarding application wrappers
peterjc authored
54 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications instead.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
55
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
56 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
57 which was declared obsolete in Release 1.54. For some time now, both the NCBI
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
58 and Biopython have encouraged people to parse the XML output instead.
59
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
60 Bio.Blast.Applications
61 ======================
62 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
63 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
7b02898 @peterjc Fixed a typo in DEPRECATED file
peterjc authored
64 1.53, having been replaced with wrappers for the new NCBI BLAST+ tools (e.g.
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
65 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
66
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
67 Bio.Clustalw
68 ============
9cbdf28 @peterjc Remove deprecated Bio.Clustalw module
peterjc authored
69 Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
70 removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
71 clustal format alignments (since Release 1.46), and Bio.Align.Applications
72 for calling the ClustalW command line tool (since Release 1.51). See the
73 Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
74
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
75 BioSQL and psycopg
76 ==================
77 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
3afd55b @peterjc Remove deprecated support for psycopg (v1) in BioSQL code
peterjc authored
78 in Release 1.51, and removed in Release 1.55. Please use psycopg2 instead.
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
79
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
80 Bio.Application.generic_run and ApplicationResult
81 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
82 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
83 Release 1.57. Please use the Python subprocess module instead, or as of
84 Release 1.55 the application wrappers can be used directly to execute the
85 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
86
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
87 Bio.Entrez.efetch and rettype="genbank"
88 =======================================
89 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
90 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
91 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
92 automatically, but issues a deprecation warning. The code to check and correct
93 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
94
95 Bio.Entrez.query function
96 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
97 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
98
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
99 Bio.SwissProt.SProt
100 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
101 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
102 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
103 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
104
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
105 Bio.Prosite and Bio.Enzyme
106 ==========================
dcbdd45 @peterjc Removing deprecated Bio.Enzyme and Bio.Prosite modules
peterjc authored
107 Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in
108 Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and
04dcf21 @peterjc Minor correction to new module name
peterjc authored
109 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
110
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
111 Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredReader
112 ================================================
113 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in
1097994 @peterjc Removing deprecated modules Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredRe...
peterjc authored
114 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
115
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
116 Bio.File
117 ========
118 Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in
119 Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated
120 in Release 1.57.
121
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
122 Bio.Graphics.GenomeDiagram and colour/color, centre/center
123 ==========================================================
124 GenomeDiagram originally used colour and centre (UK spelling of color and
125 center) for argument names. As part of its integration into Biopython 1.50,
126 this will support both colour and color, and both centre and center, to help
127 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
128 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
129 intend to eventually remove support for colour and centre in later releases
130 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
131
132 Bio.AlignAce and Bio.MEME
133 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been rem...
peterjc authored
134 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
135 in Release 1.56. Please use Bio.Motif instead.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
136
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
137 Numeric support
138 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
139 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
140 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
141
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
142 Bio.Seq and the data property
143 =============================
144 Direct use of the Seq object (and MutableSeq object) .data property is
e5fbcd7 Issue a DeprecatingWarning when accessing the .data property of Seq obje...
Michiel de Hoon authored
145 deprecated. As of Release 1.49, writing to the Seq object's .data property
146 triggered a warning, and this property was made read only in Release 1.53. In
147 Release 1.55 final, accessing the .data property gives a DeprecationWarning.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warning w...
peterjc authored
148
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
149 Bio.Transcribe and Bio.Translate
150 ================================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
151 Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
152 in Release 1.57. Please use the methods or functions in Bio.Seq instead.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
153
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
154 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
155 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and st...
peterjc authored
156 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
157 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 been...
peterjc authored
158 The three C implementations were all removed in Release 1.53. Bio.mathfns
7a92530 @peterjc Removed deprecated Bio.listfns module
peterjc authored
159 and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in
160 Release 1.57.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
161
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
162 Bio.distance (and Bio.cdistance)
163 ================================
164 Bio.distance was deprecated in Release 1.49, at which point its C code
165 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
166 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
167
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
168 Bio.Ndb
169 =======
170 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
171 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
172
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
173 Martel
174 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
175 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
176 in Release 1.51. The source code for Martel is still in our repository if
177 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
178
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
179 Bio.Mindy and associated modules.
180 =================================
181 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
182 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
183 Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.writ...
peterjc authored
184
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
185 Bio.Fasta index_file and Dictionary
186 ===================================
187 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
188 sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of
69f1dcc @peterjc Updated DEPRECATED file to reflect final name of Bio.SeqIO.index() funct...
peterjc authored
189 SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index()
8af957d @peterjc Adding the Bio.SeqIO.indexed_dict() function developed on a github branc...
peterjc authored
190 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
191
192 Bio.Fasta (including Bio.Fasta.FastaAlign)
193 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
194 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
195 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
196 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
197
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
198 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
199 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
200 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
201 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
202 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
203
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
204 Bio.Emboss.Primer
205 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Martel...
peterjc authored
206 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
207 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
208
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
209 Bio.Emboss.Applications
210 =======================
53f4841 @peterjc Remove deprecated EMBOSS PHYLIP wrappers
peterjc authored
211 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
212 obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in
213 release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g.
214 fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline,
215 EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
216 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
217 FConsenseCommandline, and FSeqBootCommandline, respectively.
218
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
219 Bio.MetaTool
220 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
221 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
222 for the output of MetaTool 3.5 which is now obsolete.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
223
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
224 Bio.GenBank
225 ===========
226 The online functionality (search_for, download_many, and NCBIDictionary) was
4f7d50c Removing the deprecated online bits of Bio.GenBank (replaced by Bio.Entr...
Peter Cock authored
227 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
228 in Release 1.54. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
229
230 Bio.PubMed
231 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
232 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
233 removed in Release 1.53. Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
234
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
235 Bio.EUtils
236 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
237 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
238
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
239 Bio.Sequencing & Bio.Medline
240 ============================
241 A revised API was added and the old one deprecated in Release 1.48,
242 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
243 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
244 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
245 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
246 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
247 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
248 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
249
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
250 Bio.Blast.NCBIWWW
251 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
252 The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52.
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
253 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
254
255 Bio.Saf
256 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
257 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
258 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
259
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
260 Bio.NBRF
261 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
262 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
263 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
264
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
265 Bio.IntelliGenetics
266 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
267 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
268 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
269
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
270 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
271 =================================================================
272 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
273 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
274 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
275
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
276 Bio.SeqIO.to_alignment()
277 ========================
278 This function was made obsolete with the introduction of Bio.AlignIO,
9eb934e @peterjc Remove deprecated Bio.SeqIO.to_alignment function
peterjc authored
279 deprecated in Release 1.54, and removed in Release 1.58. Use either the
280 Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
281 directly instead.
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
282
5e507c9 Updating for release 1.47.
mdehoon authored
283 Bio.ECell
284 =========
285 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
286 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
287
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
288 Bio.Ais
289 =======
290 Deprecated as of Release 1.45, removed in Release 1.49.
291
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
292 Bio.LocusLink
293 =============
294 Deprecated as of Release 1.45, removed in Release 1.49.
295 The NCBI's LocusLink was superseded by Entrez Gene.
296
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
297 Bio.SGMLExtractor
298 =================
299 Deprecated as of Release 1.46, removed in Release 1.49.
300
d01c450 Getting ready for release 1.46.
mdehoon authored
301 Bio.Rebase
302 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
303 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
304
305 Bio.Gobase
306 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
307 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
308
309 Bio.CDD
310 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
311 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
312
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
313 Bio.biblio
314 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
315 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
316
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
317 Bio.WWW
318 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
319 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
320 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
321 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
322
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bio.W...
peterjc authored
323 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
324 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
325 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
326
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
327 Bio.SeqIO
328 =========
329 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
330 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
331
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
332 Bio.Medline.NLMMedlineXML
333 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
334 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
335
336 Bio.MultiProc
337 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
338 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
339
340 Bio.MarkupEditor
341 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
342 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
343
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
344 Bio.lcc
345 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
346 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
347
348 Bio.crc
349 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
350 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
351
352 Bio.FormatIO
353 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
354 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
355
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
356 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
357 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
358 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
359
360 Bio.Kabat
361 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
362 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
363
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
364 Bio.SeqUtils
365 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
366 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
367 in Release 1.31, and removed in Release 1.43. Function 'translate' was
368 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
369 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
370
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
371 Function makeTableX and classes ProteinX and MissingTable were deprecated
4804f1b @peterjc Remove deprecated makeTableX function and associated classes
peterjc authored
372 in Release 1.54, and removed in Release 1.58. These were remnants of the
373 removed translate function, and no longer served any useful purpose.
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
374
3178311 @peterjc Remove deprecated SeqUtils reverse function
peterjc authored
375 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
376 removed in Release 1.58. Instead just use the string's slice method with
377 a step of minus one.
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
378
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
379 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
b6fd79e @peterjc Remove more deprecated functions in Bio.SeqUtils
peterjc authored
380 quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
381 in Release 1.58.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
382
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
383 Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
384 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
385 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
386 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
387 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
388
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
389 The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
390 in Release 1.57 (with the intention of reusing this name space for a GFF
391 parser).
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
392
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
393 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
394 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
395 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
396 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
397
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
398 Bio.SVM
399 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
400 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
401 The Support Vector Machine code in Biopython has been superceeded by a
402 more robust (and maintained) SVM library, which includes a python
403 interface. We recommend using LIBSVM:
404
405 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
406
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
407 Bio.RecordFile
408 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
409 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
410 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
411
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
412 Bio.kMeans and Bio.xkMeans
413 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
414 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
415 the function kcluster in Bio.Cluster which performs k-means or k-medians
416 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
417
418 Bio.InterPro
419 ============
420 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
421 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
422
423 Bio.SCOP
424 ========
425 The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
5af7ecc Removed Bio.SCOP.Dom.Iterator, which was deprecated
mdehoon authored
426 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
427 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56.
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
428
429 Bio.utils
430 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
431 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
432 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 this ...
peterjc authored
433 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
434 The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
435 Release 1.56, and removed in Release 1.57.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
436
437 Bio.Motif
438 =========
439 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
440 declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
441 in Release 1.57.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
442 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
443 in Release 1.53 and deprecated in Release 1.55 final; their functionality is
40ff78e Updating the DEPRECATED file concerning the parser simplifications in Bi...
mdehoon authored
444 now available through a read() function in Bio.Motif.Parsers.AlignAce.
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
445 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
446 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
447 deprecated in Release 1.55 final; their functionality is now available through
448 a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
449 respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace RecordPa...
mdehoon authored
450
451 Bio.Compass
452 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
453 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
c4d0fa8 @peterjc Remove deprecated bits of Bio.Compass
peterjc authored
454 deprecated in Release 1.55, removed in Release 1.59. Their functionality is
455 now available through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
456
457 Bio.Affy.CelFile
458 ================
459 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
460 in Release 1.54. Their functionality is now available through a read()
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
461 function. These classes were deprecated in Release 1.55 final.
815d64f making the obsolete classes more explicit
mdehoon authored
462
463 Bio.PopGen.FDist
464 ================
465 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
3704a68 @peterjc Update NEWS and DEPRECATED files
peterjc authored
466 in Release 1.54, deprecated in Release 1.55, and removed in Release 1.58.
467 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
468
469 Bio.UniGene
470 ===========
471 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
472 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
473 Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release
474 1.55 final. Their functionality is now available through a read() and a parse()
475 function in Bio.UniGene.
815d64f making the obsolete classes more explicit
mdehoon authored
476
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
477 Bio.SubsMat
478 ===========
479 The methods letter_sum and all_letters_sum were removed from the SeqMat class in
480 Bio.SubsMat in Release 1.57.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
481
482 Bio.Align
483 =========
484 The methods get_column and add_sequence of the MultipleSeqAlignment class were
485 deprecated in Release 1.57. The Alignment class in Bio.Align.Generic and its
486 method get_seq_by_num were deprecated in Release 1.57.
Something went wrong with that request. Please try again.