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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
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
c52e986 @peterjc Make Bio.SeqFeature position objects act like and subclass int
peterjc authored
15 Bio.SeqFeature.WithinPosition and OneOfPosition
16 ===============================================
17 The arguments to create these fuzzy positions changed in Release 1.59.
18
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
19 Bio.Encodings
20 =============
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
21 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
22 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
23
24 Bio.PropertyManager
25 ===================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
26 Explicitly declared obsolete in Release 1.55, deprecated in Release 1.56, and
27 removed in Release 1.57.
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
28
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
29 Bio.InterPro
30 ============
4749068 @peterjc Remove deprecated Bio.InterPro module (HTML parser)
peterjc authored
31 This module was a parser for the EBI InterPro webpages, but no longer worked
32 with their current website. Deprecated in Release 1.55, and removed in
33 Release 1.58.
9971d2c @peterjc Deprecating Bio.InterPro since it doesn't work with the current EBI Inte...
peterjc authored
34
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
35 Bio.GenBank.LocationParser
36 ==========================
37 This module used to be used for parsing GenBank and EMBL feature locations.
38 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
39 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
40
41 Bio.Parsers and Bio.Parsers.spark
42 =================================
43 This module was a copy of John Aycock's SPARK parser included with Biopython
f38249a @peterjc Fixed a typo
peterjc authored
44 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
45 1.55, deprecated in Release 1.56.
1b7544b @peterjc Declare Bio.GenBank.LocationParser, Bio.Parsers.spark and Bio.Parsers as...
peterjc authored
46
d52e8d4 @peterjc Replacing Bio.Restriction.DNAUtils C code with pure python and deprecati...
peterjc authored
47 Bio.Restriction.DNAUtils and check_bases
48 ========================================
49 This module (originally in C) offered complement and antiparallel functions
50 (duplicating functionality in Bio.Seq) and a rather odd function called
51 check_bases (also available as Bio.Restriction.Restriction.check_bases).
e0e37e1 @peterjc Remove deprecated Bio.Restriction.DNAUtils and check_bases
peterjc authored
52 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
53
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
54 Bio.Blast.NCBIStandalone
55 ========================
56 The three functions for calling the "legacy" NCBI BLAST command line tools
57 blastall, blastpgp and rpsblast were declared obsolete in Biopython Release
ad5ea06 @peterjc Clarify DEPRECATED file regarding application wrappers
peterjc authored
58 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
59
b308b4c @peterjc Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing l...
peterjc authored
60 The remainder of this module is a parser for the plain text BLAST output,
db24ce4 @peterjc Fixed a typo
peterjc authored
61 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
62 and Biopython have encouraged people to parse the XML output instead.
63
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
64 Bio.Blast.Applications
65 ======================
66 NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,
67 BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release
7b02898 @peterjc Fixed a typo in DEPRECATED file
peterjc authored
68 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
69 NcbiblastpCommandline and NcbipsiblastCommandline).
2ed247a @peterjc Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as obso...
peterjc authored
70
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
71 Bio.Clustalw
72 ============
9cbdf28 @peterjc Remove deprecated Bio.Clustalw module
peterjc authored
73 Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
74 removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
75 clustal format alignments (since Release 1.46), and Bio.Align.Applications
76 for calling the ClustalW command line tool (since Release 1.51). See the
77 Tutorial for examples.
0caf433 @peterjc Explicitly say that Bio.Clustalw is now obsolete, with a doctest example...
peterjc authored
78
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
79 BioSQL and psycopg
80 ==================
81 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
82 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
83
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
84 Bio.Application.generic_run and ApplicationResult
85 =================================================
57b6b9d @peterjc Removed deprecated Bio.Application.generic_run and ApplicationResult
peterjc authored
86 Declared obsolete in Release 1.51, deprecated in Release 1.53, and removed in
87 Release 1.57. Please use the Python subprocess module instead, or as of
88 Release 1.55 the application wrappers can be used directly to execute the
89 command.
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
90
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
91 Bio.Entrez.efetch and rettype="genbank"
92 =======================================
93 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
94 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
95 (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this
8dc3666 Removing the deprecated code
Michiel de Hoon authored
96 automatically, but issues a deprecation warning. The code to check and correct
97 for "genbank" was removed in Biopython 1.55 final.
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
98
99 Bio.Entrez.query function
100 =========================
63aa633 @peterjc State the the legacy BLAST wrappers in Bio.Blast.Applications are obsole...
peterjc authored
101 Deprecated in Release 1.47, removed in Release 1.52.
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
102
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
103 Bio.SwissProt.SProt
104 ===================
f21c46d Removing Bio.SwissProt.SProt, which was deprecated
mdehoon authored
105 Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in
106 Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available
107 from Bio.SwissProt.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
108
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
109 Bio.Prosite and Bio.Enzyme
110 ==========================
dcbdd45 @peterjc Removing deprecated Bio.Enzyme and Bio.Prosite modules
peterjc authored
111 Declared obsolete in Release 1.50, deprecated in Release 1.53, and removed in
112 Release 1.57. Most of the functionality has moved to Bio.ExPASy.Prosite and
04dcf21 @peterjc Minor correction to new module name
peterjc authored
113 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
114
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
115 Bio.EZRetrieve, Bio.NetCatch, Bio.FilteredReader
116 ================================================
117 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
118 Release 1.56.
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
119
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
120 Bio.File
121 ========
122 Bio.File.SGMLHandle was declared obsolete in Release 1.50, deprecated in
123 Release 1.52, and removed in Release 1.56. Bio.File.SGMLStripper was deprecated
484b3e6 Deprecating Bio.ParserSupport.SGMLStrippingConsumer
Michiel de Hoon authored
124 in Release 1.57. Bio.File.StringHandle was deprecated in Release 1.59.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
125
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
126 Bio.Graphics.GenomeDiagram and colour/color, centre/center
127 ==========================================================
128 GenomeDiagram originally used colour and centre (UK spelling of color and
129 center) for argument names. As part of its integration into Biopython 1.50,
130 this will support both colour and color, and both centre and center, to help
131 people port existing scripts written for the standalone version of
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
132 GenomeDiagram. However, these were deprecated in Release 1.55 final, and we
133 intend to eventually remove support for colour and centre in later releases
134 of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes chan...
peterjc authored
135
136 Bio.AlignAce and Bio.MEME
137 =========================
b19dee9 @peterjc Updated DEPRECATED file now that Bio.AlignAce and Bio.MEME have been rem...
peterjc authored
138 Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed
139 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
140
2669c4d - Updates to move from Numeric python to NumPy. Python modules have back...
chapmanb authored
141 Numeric support
142 ===============
362d4c5 @peterjc Making Seq.data read only
peterjc authored
143 Following the Release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
144 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
145
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
146 Bio.Seq and the data property
147 =============================
148 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
149 deprecated. As of Release 1.49, writing to the Seq object's .data property
150 triggered a warning, and this property was made read only in Release 1.53. In
151 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
152
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to be ...
peterjc authored
153 Bio.Transcribe and Bio.Translate
154 ================================
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
155 Declared obsolete in Release 1.49, deprecated in Release 1.51, and removed
156 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
157
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
158 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
159 ==========================================
2b025ba @peterjc Removing C implementations of deprecated modules listfns, mathfns and st...
peterjc authored
160 Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were
161 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
162 The three C implementations were all removed in Release 1.53. Bio.mathfns
7a92530 @peterjc Removed deprecated Bio.listfns module
peterjc authored
163 and Bio.stringfns were removed in Release 1.55. Bio.listfns was removed in
164 Release 1.57.
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C implementa...
peterjc authored
165
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
166 Bio.distance (and Bio.cdistance)
167 ================================
168 Bio.distance was deprecated in Release 1.49, at which point its C code
169 implementation Bio.cdistance was removed (this was not intended as a public
0c62520 @peterjc Removing Bio.distance (deprecated in Biopython 1.49)
peterjc authored
170 API). Removed in Release 1.53.
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2724...
peterjc authored
171
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
172 Bio.Ndb
173 =======
174 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
175 Removed in Release 1.53.
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
176
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
177 Martel
178 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
179 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
180 in Release 1.51. The source code for Martel is still in our repository if
181 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
182
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
183 Bio.Mindy and associated modules.
184 =================================
185 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
186 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
187 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
188
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
189 Bio.Fasta index_file and Dictionary
190 ===================================
191 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
192 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
193 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
194 which is suitable even for very large files.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
195
196 Bio.Fasta (including Bio.Fasta.FastaAlign)
197 ==========================================
e9a7cd6 Removing the deprecated module Bio.Fasta
Michiel de Hoon authored
198 Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed
199 in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or
200 Bio.AlignIO instead.
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
201
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
202 Bio.Align.FormatConvert
6128014 @peterjc Note Bio.Encodings, Bio.PropertyManager and Bio.utils are obsolete in DE...
peterjc authored
203 ======================
0433a74 Removing the deprecated module Bio.Align.FormatConvert
Michiel de Hoon authored
204 Declared obsolete in Release 1.48, deprecated in Release 1.51, and
205 removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment
206 object's format method instead.
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bio.A...
peterjc authored
207
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
208 Bio.Emboss.Primer
209 =================
6aa0b3a @peterjc Removing deprecated Bio.Emboss.Primer3 module (and the associated Martel...
peterjc authored
210 Deprecated in Release 1.48, and removed in Release 1.51, this parser was
211 replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
212
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
213 Bio.Emboss.Applications
214 =======================
53f4841 @peterjc Remove deprecated EMBOSS PHYLIP wrappers
peterjc authored
215 The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared
216 obsolete in Biopython 1.52, deprecated in Release 1.55 final, and removed in
217 release 1.58. please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g.
218 fneighbor) instead. Specifically, EProtDistCommandline, ENeighborCommandline,
219 EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline are
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
220 replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline,
221 FConsenseCommandline, and FSeqBootCommandline, respectively.
222
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about this...
peterjc authored
223 Bio.MetaTool
224 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
225 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
226 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
227
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE, an...
peterjc authored
228 Bio.GenBank
229 ===========
230 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
231 declared obsolete in Release 1.48, deprecated in Release 1.50, and removed
232 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
233
234 Bio.PubMed
235 ==========
cf8b55c @peterjc Removing deprecated module Bio.PubMed (use Bio.Entrez instead)
peterjc authored
236 Declared obsolete in Release 1.48, deprecated in Release 1.49, and
237 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
238
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
239 Bio.EUtils
240 ==========
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
241 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
242
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
243 Bio.Sequencing & Bio.Medline
244 ============================
245 A revised API was added and the old one deprecated in Release 1.48,
246 and removed in Biopython 1.52:
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
247 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
248 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
249 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
250 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
251 Bio.Medline.RecordParser --> Bio.Medline.read(handle)
252 Bio.Medline.Iterator --> Bio.Medline.parse(handle)
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
253
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
254 Bio.Blast.NCBIWWW
255 =================
2619bcb @peterjc Update DEPRECATED file after Bio.EUtils removal etc
peterjc authored
256 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
257 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
258
259 Bio.Saf
260 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
261 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
262 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
263
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
264 Bio.NBRF
265 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
266 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
267 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
268
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
269 Bio.IntelliGenetics
270 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
271 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
272 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
273
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Align...
peterjc authored
274 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
275 =================================================================
276 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
277 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
278 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
279
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
280 Bio.SeqIO.to_alignment()
281 ========================
282 This function was made obsolete with the introduction of Bio.AlignIO,
9eb934e @peterjc Remove deprecated Bio.SeqIO.to_alignment function
peterjc authored
283 deprecated in Release 1.54, and removed in Release 1.58. Use either the
284 Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class
285 directly instead.
497ae00 @peterjc Deprecating already obsolete function Bio.SeqIO.to_alignment()
peterjc authored
286
5e507c9 Updating for release 1.47.
mdehoon authored
287 Bio.ECell
288 =========
289 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
290 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
291
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
292 Bio.Ais
293 =======
294 Deprecated as of Release 1.45, removed in Release 1.49.
295
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the NCB...
peterjc authored
296 Bio.LocusLink
297 =============
298 Deprecated as of Release 1.45, removed in Release 1.49.
299 The NCBI's LocusLink was superseded by Entrez Gene.
300
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
301 Bio.SGMLExtractor
302 =================
303 Deprecated as of Release 1.46, removed in Release 1.49.
304
d01c450 Getting ready for release 1.46.
mdehoon authored
305 Bio.Rebase
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.Gobase
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
313 Bio.CDD
314 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebase w...
peterjc authored
315 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
316
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember to u...
peterjc authored
317 Bio.biblio
318 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
319 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
320
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
321 Bio.WWW
322 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
323 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
324 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48,
325 and removed in Release 1.53.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were remo...
peterjc authored
326
398aa6f @peterjc Updated the DEPRECATED file to mention Bio.Entrez replaced the old Bio.W...
peterjc authored
327 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and
328 Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and
329 Bio.Entrez instead.
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
330
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
331 Bio.SeqIO
332 =========
333 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
334 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
335
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
336 Bio.Medline.NLMMedlineXML
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.MultiProc
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
344 Bio.MarkupEditor
345 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
346 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
347
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
348 Bio.lcc
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.lcc in Release 1.44, removed in 1.46.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
351
352 Bio.crc
353 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
354 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
355
356 Bio.FormatIO
357 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
358 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
359
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
360 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
361 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
362 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
363
364 Bio.Kabat
365 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
366 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
367
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
368 Bio.SeqUtils
369 ============
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
370 Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated
371 in Release 1.31, and removed in Release 1.43. Function 'translate' was
372 deprecated in Release 1.49, and removed in Release 1.53. Use the functions
373 and methods in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq's S...
mdehoon authored
374
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
375 Function makeTableX and classes ProteinX and MissingTable were deprecated
4804f1b @peterjc Remove deprecated makeTableX function and associated classes
peterjc authored
376 in Release 1.54, and removed in Release 1.58. These were remnants of the
377 removed translate function, and no longer served any useful purpose.
8135f46 @peterjc Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and MissingT...
peterjc authored
378
3178311 @peterjc Remove deprecated SeqUtils reverse function
peterjc authored
379 Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
380 removed in Release 1.58. Instead just use the string's slice method with
381 a step of minus one.
0d6a55c @peterjc Deprecating Bio.SeqUtils.reverse() function
peterjc authored
382
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
383 Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
b6fd79e @peterjc Remove more deprecated functions in Bio.SeqUtils
peterjc authored
384 quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
385 in Release 1.58.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
386
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
387 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
388 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
389 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
390 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
391 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
392
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
393 The whole of the old Bio.GFF module was deprecated in Release 1.53, and removed
394 in Release 1.57 (with the intention of reusing this name space for a GFF
395 parser).
dc5c326 @peterjc Deprecating Bio.GFF as discussed on the mailing list
peterjc authored
396
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse were ...
chapmanb authored
397 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
398 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
399 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
400 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
401
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
402 Bio.SVM
403 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added mi...
peterjc authored
404 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
405 The Support Vector Machine code in Biopython has been superceeded by a
406 more robust (and maintained) SVM library, which includes a python
407 interface. We recommend using LIBSVM:
408
409 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
410
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
411 Bio.RecordFile
412 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
413 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
414 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
415
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
416 Bio.kMeans and Bio.xkMeans
417 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from Bio...
peterjc authored
418 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
419 the function kcluster in Bio.Cluster which performs k-means or k-medians
420 clustering.
0281cb8 Removing the deprecated function pairlist_to_dict from Bio.InterPro
mdehoon authored
421
422 Bio.InterPro
423 ============
424 The function pairlist_to_dict was deprecated in Release 1.45, and removed in
425 Release 1.53.
26b1d47 Removing the deprecated module Bio.SCOP.FileIndex
mdehoon authored
426
427 Bio.SCOP
428 ========
429 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
430 Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55
431 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
432
433 Bio.utils
434 =========
ae3349d @peterjc Mention deprecation of Bio.utils.ungap and fixing some long lines in the...
peterjc authored
435 Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
999d2e4 removed the deprecated functions translate, translate_to_stop, back_tran...
mdehoon authored
436 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
437 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead.
87f1c8f Updated the file DEPRECATED
Michiel de Hoon authored
438 The whole of Bio.utils was declared obsolete in Release 1.55, deprecated in
439 Release 1.56, and removed in Release 1.57.
31f6097 Deprecating CompareAce paresr from Bio.Motif module
bartek authored
440
441 Bio.Motif
442 =========
443 CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
444 declared obsolete in Release 1.53, deprecated in Release 1.55 final, and removed
445 in Release 1.57.
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
446 AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
447 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
448 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
449 MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
450 _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
451 deprecated in Release 1.55 final; their functionality is now available through
452 a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
453 respectively.
e463061 In Bio.Compass, add a read() and a parse() function to replace RecordPa...
mdehoon authored
454
455 Bio.Compass
456 ===========
8537d62 Adding DeprecationWarnings to obsolete code
Michiel de Hoon authored
457 The RecordParser and Iterator classes were declared obsolete in Release 1.54,
c4d0fa8 @peterjc Remove deprecated bits of Bio.Compass
peterjc authored
458 deprecated in Release 1.55, removed in Release 1.59. Their functionality is
459 now available through a read() and a parse() function, respectively.
815d64f making the obsolete classes more explicit
mdehoon authored
460
461 Bio.Affy.CelFile
462 ================
463 The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete
9dfbc94 @peterjc Remove deprecated bits of Bio.Affy.CelFile
peterjc authored
464 in Release 1.54, deprecated in Release 1.55 and removed in Release 1.59.
465 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
466
467 Bio.PopGen.FDist
468 ================
469 The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
3704a68 @peterjc Update NEWS and DEPRECATED files
peterjc authored
470 in Release 1.54, deprecated in Release 1.55, and removed in Release 1.58.
471 Their functionality is now available through a read() function.
815d64f making the obsolete classes more explicit
mdehoon authored
472
473 Bio.UniGene
474 ===========
475 The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord,
476 UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
477 Bio.UniGene were declared obsolete in Release 1.54, deprecated in Release 1.55,
ecdde52 @peterjc Correct typo in last commit
peterjc authored
478 and removed in Release 1.59. Their functionality is now available through a
860cc94 @peterjc Removing deprecated bits of Bio.UniGene
peterjc authored
479 read() and a parse() function in Bio.UniGene.
c13d64d Updating comments and DEPRECATED file
Michiel de Hoon authored
480 The HTML parser in Bio.UniGene.UniGene was declared obsolete in Release 1.59.
815d64f making the obsolete classes more explicit
mdehoon authored
481
f019593 Removing deprecated code that won't be in Release 1.57
mdehoon authored
482 Bio.SubsMat
483 ===========
484 The methods letter_sum and all_letters_sum were removed from the SeqMat class in
485 Bio.SubsMat in Release 1.57.
855675b Replacing PendingDeprecationWarnings with BiopythonDeprecationWarnings
Michiel de Hoon authored
486
487 Bio.Align
488 =========
489 The methods get_column and add_sequence of the MultipleSeqAlignment class were
490 deprecated in Release 1.57. The Alignment class in Bio.Align.Generic and its
491 method get_seq_by_num were deprecated in Release 1.57.
c13d64d Updating comments and DEPRECATED file
Michiel de Hoon authored
492
493 Bio.ParserSupport
494 =================
495 Bio.ParserSupport was declared obsolete in Release 1.59.
484b3e6 Deprecating Bio.ParserSupport.SGMLStrippingConsumer
Michiel de Hoon authored
496 Bio.ParserSupport.SGMLStrippingConsumer was deprecated in Release 1.59.
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