This file provides documentation for modules in Biopython that have been moved or deprecated in favor of other modules. This provides some quick and easy to find documentation about how to update your code to work again. Python 2.3 ========== No longer supported as of Release 1.51, having triggered a warning with Release 1.50, with a mention in the release notes for Release 1.49. Python 2.4 ========== As of Biopython 1.54, we consider support for Python 2.4 to be deprecated. This means we will continue to support Python 2.4 for at least two further releases, and at least one year (whichever takes longer), before dropping support for Python 2.4. This can be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries). An explicit warning was added to setup.py for Biopython 1.55. Bio.Encodings ============= Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56. Bio.PropertyManager =================== Explicitly declared obsolete in Release 1.55, and deprecated in Release 1.56. Bio.InterPro ============ This module was a parser for the EBI InterPro webpages, but no longer works with their current website. Deprecated in Release 1.55. Bio.GenBank.LocationParser ========================== This module used to be used for parsing GenBank and EMBL feature locations. It has been replaced with faster code using regular expressions, and is no longer needed. Declared obsolete in Release 1.55, deprecated in Release 1.56. Bio.Parsers and Bio.Parsers.spark ================================= This module was a copy of John Aycock's SPARK parser included with Biopython soley for use in Bio.GenBank.LocationParser. Declared obsolete in Release 1.55, deprecated in Release 1.56. Bio.Restriction.DNAUtils and check_bases ======================================== This module (originally in C) offered complement and antiparallel functions (duplicating functionality in Bio.Seq) and a rather odd function called check_bases (also available as Bio.Restriction.Restriction.check_bases). Deprecated in Release 1.53. Bio.Blast.NCBIStandalone ======================== The three functions for calling the "legacy" NCBI BLAST command line tools blastall, blastpgp and rpsblast were declared obsolete in Biopython Release 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications instead. The remainder of this module is a parser for the plain text BLAST output, which was declared obsolete in Release 1.54. For some time now, both the NCBI and Biopython have encouraged people to parse the XML output instead. Bio.Blast.Applications ====================== NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline, BlastpgpCommandline and RpsBlastCommandline were declared obsolete in Release 1.53, having been replace with wrappers for the new NCBI BLAST+ tools (e.g. NcbiblastpCommandline and NcbipsiblastCommandline). Bio.EMBOSS.Applications ======================= The wrappers for the "old" EMBOSS PHYLIP tools (e.g. eneighbor) were declared obsolete in Biopython 1.52, please use the wrappers for the "new" EMBOSS PHYLIP tools (e.g. fneighbor) instead. Bio.Clustalw ============ Declared obsolete in Release 1.52, and deprecated in Release 1.55 final, having been replaced with Bio.AlignIO for parsing and writing clustal format alignments (since Release 1.46), and Bio.Align.Applications for calling the ClustalW command line tool (Release 1.51). See the Tutorial for examples. BioSQL and psycopg ================== Support for psycopg (version one) in Biopython's BioSQL code was deprecated in Release 1.51, and removed in Release 1.55. Please use psycopg2 instead. Bio.Application.generic_run and ApplicationResult ================================================= Declared obsolete in Release 1.51, and deprecated in Release 1.53. Please use the Python subprocess module instead, of as of Release 1.55 the application wrappers can be used directly to execute the command. Bio.Entrez.efetch and rettype="genbank" ======================================= As of Easter 2009, the NCBI have stopped supporting the unofficial return type of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp" (GenPept). As of Biopython 1.50, Bio.Entrez.efetch will correct this automatically, but issues a deprecation warning. The code to check and correct for "genbank" was removed in Biopython 1.55 final. Bio.Entrez.query function ========================= Deprecated in Release 1.47, removed in Release 1.52. Bio.SwissProt.SProt =================== Declared obsolete in Release 1.50, deprecated in Release 1.51, and removed in Release 1.56. Most of the functionality in Bio.SwissProt.SProt is available from Bio.SwissProt. Bio.Prosite and Bio.Enzyme ========================== Declared obsolete in Release 1.50, and deprecated in Release 1.53. Most of the functionality has moved to Bio.ExPASy.Prosite and Bio.ExPASy.Enzyme, respectively. Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader ===================================================================== Declared obsolete in Release 1.50, deprecated in Release 1.52, removed in Release 1.56. Bio.Graphics.GenomeDiagram and colour/color, centre/center ========================================================== GenomeDiagram originally used colour and centre (UK spelling of color and center) for argument names. As part of its integration into Biopython 1.50, this will support both colour and color, and both centre and center, to help people port existing scripts written for the standalone version of GenomeDiagram. However, these were deprecated in Release 1.55 final, and we intend to eventually remove support for colour and centre in later releases of Biopython. Bio.AlignAce and Bio.MEME ========================= Declared obsolete in Release 1.50, deprecated in Release 1.52, and removed in Release 1.56. Please use Bio.Motif instead. Numeric support =============== Following the Release of 1.48, Numeric support in Biopython is discontinued. Please move to NumPy for Biopython 1.49 or later. Bio.Seq and the data property ============================= Direct use of the Seq object (and MutableSeq object) .data property is deprecated. As of Release 1.49, writing to the Seq object's .data property triggered a warning, and this property was made read only in Release 1.53. In Release 1.55 final, accessing the .data property gives a DeprecationWarning. Bio.Transcribe and Bio.Translate ================================ Declared obsolete in Release 1.49, deprecated in Release 1.51. Please use the methods or functions in Bio.Seq instead. Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants) ========================================== Declared obsolete in Release 1.49. Bio.mathfns and Bio.stringfns were deprecated in Release 1.50, Bio.listfns was deprecated in Release 1.53. The three C implementations were all removed in Release 1.53. Bio.mathfns and Bio.stringfns were removed in Release 1.55. Bio.distance (and Bio.cdistance) ================================ Bio.distance was deprecated in Release 1.49, at which point its C code implementation Bio.cdistance was removed (this was not intended as a public API). Removed in Release 1.53. Bio.Ndb ======= Deprecated in Release 1.49, as the website this parsed has been redesigned. Removed in Release 1.53. Martel ====== Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed in Release 1.51. The source code for Martel is still in our repository if anyone wanted to develop this outside of Biopython. Bio.Mindy and associated modules. ================================= Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders, Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules Bio.Fasta index_file and Dictionary =================================== Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of SeqRecord objects. Biopython 1.52 onwards provides Bio.SeqIO.index() which is suitable even for very large files. Bio.Fasta (including Bio.Fasta.FastaAlign) ========================================== Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed in Release 1.55 final. Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead. Bio.Align.FormatConvert ====================== Declared obsolete in Release 1.48, deprecated in Release 1.51, and removed in Release 1.55 final. Please use Bio.AlignIO or the Alignment object's format method instead. Bio.Emboss.Primer ================= Deprecated in Release 1.48, and removed in Release 1.51, this parser was replaced by Bio.Emboss.Primer3 and Bio.Emboss.PrimerSearch instead. Bio.Emboss.Applications ======================= EProtDistCommandline, ENeighborCommandline, EProtParsCommandline, EConsenseCommandline, and ESeqBootCommandline were declared obsolete in Release 1.52, and deprecated in Release 1.55 final. These functions were replaced by FProtDistCommandline, FNeighborCommandline, FProtParsCommandline, FConsenseCommandline, and FSeqBootCommandline, respectively. Bio.MetaTool ============ Deprecated in Release 1.48, and removed in Release 1.51, this was a parser for the output of MetaTool 3.5 which is now obsolete. Bio.GenBank =========== The online functionality (search_for, download_many, and NCBIDictionary) was declared obsolete in Release 1.48, deprecated in Release 1.50, and removed in Release 1.54. Please use Bio.Entrez instead. Bio.PubMed ========== Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed in Release 1.53. Please use Bio.Entrez instead. Bio.EUtils ========== Deprecated in favor of Bio.Entrez in Release 1.48, removed in Release 1.52. Bio.Sequencing & Bio.Medline ============================ A revised API was added and the old one deprecated in Release 1.48, and removed in Biopython 1.52: Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle) Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle) Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle) Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle) Bio.Medline.RecordParser --> Bio.Medline.read(handle) Bio.Medline.Iterator --> Bio.Medline.parse(handle) Bio.Blast.NCBIWWW ================= The HTML BLAST parser was deprecated in Release 1.48, and removed in 1.52. The deprecated functions blast and blasturl were removed in Release 1.44. Bio.Saf ======= Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser for this "simple alignment format" could be developed for Bio.AlignIO instead. Bio.NBRF ======== Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO, removed in Release 1.51. Bio.IntelliGenetics =================== Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO, removed in Release 1.51. Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO ================================================================= You can still use the "phylip", "clustal", "nexus" and "stockholm" formats in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49. Bio.SeqIO.to_alignment() ======================== This function was made obsolete with the introduction of Bio.AlignIO, and deprecated in Release 1.54. Use either the Bio.AlignIO functions, or the Bio.Align.MultipleSeqAlignment class directly instead. Bio.ECell ========= Deprecated as of Release 1.47, as it appears to have no users, and the code does not seem relevant for ECell 3. Removed in Release 1.49. Bio.Ais ======= Deprecated as of Release 1.45, removed in Release 1.49. Bio.LocusLink ============= Deprecated as of Release 1.45, removed in Release 1.49. The NCBI's LocusLink was superseded by Entrez Gene. Bio.SGMLExtractor ================= Deprecated as of Release 1.46, removed in Release 1.49. Bio.Rebase ========== Deprecated as of Release 1.46, removed in Release 1.49. Bio.Gobase ========== Deprecated as of Release 1.46, removed in Release 1.49. Bio.CDD ======= Deprecated as of Release 1.46, removed in Release 1.49. Bio.biblio ========== Deprecated as of Release 1.45, removed in Release 1.48 Bio.WWW ======= The modules under Bio.WWW were deprecated in Release 1.45, and removed in Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48, and removed in Release 1.53. The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro, Bio.WWW.ExPASy and Bio.WWW.NCBI is now available from Bio.SCOP, Bio.InterPro, Bio.ExPASy and Bio.Entrez instead. Bio.SeqIO ========= The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of the new Bio.SeqIO module as of Release 1.44, removed in Release 1.47. Bio.Medline.NLMMedlineXML ========================= Deprecated in Release 1.44, removed in 1.46. Bio.MultiProc ============= Deprecated in Release 1.44, removed in 1.46. Bio.MarkupEditor ================ Deprecated in Release 1.44, removed in 1.46. Bio.lcc ======= Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44, removed in 1.46. Bio.crc ======= Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44, removed in 1.46. Bio.FormatIO ============ This was removed in Release 1.44 (a deprecation was not possible). Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs ====================================================================== These were deprecated in Release 1.44, and removed in Release 1.49. Bio.Kabat ========= This was deprecated in Release 1.43 and removed in Release 1.44. Bio.SeqUtils ============ Functions 'complement' and 'antiparallel' in Bio.SeqUtils were deprecated in Release 1.31, and removed in Release 1.43. Function 'translate' was deprecated in Release 1.49, and removed in Release 1.53. Use the functions and methods in Bio.Seq instead. Function makeTableX and classes ProteinX and MissingTable were deprecated in Release 1.54. These were remnants of the removed translate function, and no longer served any useful purpose. Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead just use the string's slice method with a step of minus one. Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and quicker_apply_on_multi_fasta were deprecated in Release 1.55 final. Bio.GFF (for accessing a MySQL database created with BioPerl, etc) ======= The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have been deprecated as of Release 1.31, and removed in Release 1.43. Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead. The whole of the old Bio.GFF module was deprecated in Release 1.53 (with the intention of reusing this name space for a GFF parser). Bio.sequtils ============ Deprecated as of Release 1.30, removed in Release 1.42. Use Bio.SeqUtils instead. Bio.SVM ======= Deprecated as of Release 1.30, removed in Release 1.42. The Support Vector Machine code in Biopython has been superceeded by a more robust (and maintained) SVM library, which includes a python interface. We recommend using LIBSVM: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ Bio.RecordFile ============== Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't completely implemented and duplicates the work of most standard parsers. Bio.kMeans and Bio.xkMeans ========================== Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use the function kcluster in Bio.Cluster which performs k-means or k-medians clustering. Bio.InterPro ============ The function pairlist_to_dict was deprecated in Release 1.45, and removed in Release 1.53. Bio.SCOP ======== The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in Release 1.53. The class Parser in Bio.SCOP.Dom was removed in Release 1.55 final. The class Iterator in Bio.SCOP.Dom was removed in Release 1.56. Bio.utils ========= Functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe', and 'back_transcribe' were deprecated in Release 1.49, and removed in Release 1.53. Function 'ungap' was deprecated in Release 1.53. Use Bio.Seq instead. The whole of Bio.utils was declared obsolete in Release 1.55, and deprecated in Biopython 1.56. Bio.Motif ========= CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were declared obsolete in Release 1.53, and deprecated in Release 1.55 final. AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete in Release 1.53 and deprecated in Release 1.55 final; their functionality is now available through a read() function in Bio.Motif.Parsers.AlignAce. MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser, _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and deprecated in Release 1.55 final; their functionality is now available through a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST, respectively. Bio.Compass =========== The RecordParser and Iterator classes were declared obsolete in Release 1.54, and deprecated in Release 1.55 final. Their functionality is now available through a read() and a parse() function, respectively. Bio.Affy.CelFile ================ The CelScanner, CelConsumer, CelRecord, and CelParser were declared obsolete in Release 1.54. Their functionality is now available through a read() function. These classes were deprecated in Release 1.55 final. Bio.PopGen.FDist ================ The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete in Release 1.54, and deprecated in Release 1.55 final. Their functionality is now available through a read() function. Bio.UniGene =========== The classes UnigeneSequenceRecord, UnigeneProtsimRecord, UnigeneSTSRecord, UnigeneRecord, _RecordConsumer, _Scanner, RecordParser, and Iterator in Bio.UniGene were declared obsolete in Release 1.54, and deprecated in Release 1.55 final. Their functionality is now available through a read() and a parse() function in Bio.UniGene.
