DEPRECATED

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.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. Declated obsolete in Release 1.55.

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. Declated obsolete in Release
1.55.

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 and the Python
subprocess module 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, 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, 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.

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.

Bio.Entrez.query function
=========================
Deprecated in Release 1.47, removed in Release 1.52.

Bio.SwissProt.SProt
===================
Declared obsolete in Release 1.50, and deprecated in Release 1.51. 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.

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
=========================
Declared obsolete in Release 1.50, and deprecated in Release 1.52. 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, and deprecated in Release 1.51.
Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.

Bio.Align.FormatConvert
=======================
Declared obsolete in Release 1.48, and deprecated in Release 1.51.
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.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.

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.

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.

Bio.Motif
=========
CompareAceParser and CompareAceConsumer from Bio.Motif.Parsers.AlignAce were
deprecated in Release 1.53. AlignAceConsumer, AlignAceParser, and
AlignAceScanner were declared obsolete in Release 1.53; 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; 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.
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.

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. Their functionality is now
available through a read() and a parse() function in Bio.UniGene.