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DEPRECATED
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DEPRECATED
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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.
Bio.Prosite and Bio.Enzyme
==========================
Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
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, will be deprecated in a subsequent release.
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, we do intend to deprecate and then eventually
remove support for colour and centre in later releases of Biopython.
Bio.AlignAce and Bio.MEME
=========================
As of Biopython 1.50, these modules are considered to be obsolete with the
introduction of Bio.Motif, and they will be deprecated in a future release.
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
discouraged. As of release 1.49, writing to the Seq object's .data property
triggers a warning, and this property is likely to be made read only in the
next release.
Bio.Transcribe and Bio.Translate
================================
Declared obsolete in Release 1.49.
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
(the deprecation of Bio.listfns is still pending)
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).
Bio.Ndb
=======
Deprecated in Release 1.49, as the website this parsed has been redesigned.
Martel
======
Declared obsolete in Release 1.48, deprecated in Release 1.49.
Bio.Mindy
=========
Declared obsolete in Release 1.48, deprecated in Release 1.49.
Bio.builders, Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef
================================================================
Part of the Martel/Mindy parsing infrastructure, these were deprecated in
Release 1.49.
Bio.Writer and Bio.writers
==========================
Deprecated in Release 1.48.
Bio.Emboss.Primer
=================
Deprecated in Release 1.48, this parser was replaced by Bio.Emboss.Primer3
and Bio.Emboss.PrimerSearch instead.
Bio.MetaTool
============
Deprecated in Release 1.48, 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, and deprecated in Release 1.50.
Please use Bio.Entrez instead.
Bio.PubMed
==========
Declared obsolete in Release 1.48, deprecated in Release 1.49.
Please use Bio.Entrez instead.
Bio.EUtils
==========
Deprecated in favor of Bio.Entrez in Release 1.48.
Bio.Sequencing
==============
A revised API was added and the old one deprecated in Biopython 1.48:
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.Blast.NCBIWWW
=================
The HTML BLAST parser was deprecated as of Release 1.48.
The deprecated functions blast and blasturl were removed in Release 1.44.
Bio.Saf
=======
Deprecated as of Release 1.48, as it appears to have no users, and relies
on Martel which doesn't work properly with mxTextTools 3.0.
Bio.NBRF
========
Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO
Bio.IntelliGenetics
===================
Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO
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.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.
The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy 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
============
The functions 'complement' and 'antiparallel' in Bio.SeqUtils 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.
Bio.GFF
=======
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.
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.