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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.
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.
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, please use 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 1.52.
Bio.SwissProt.SProt
===================
Declared obsolete in Release 1.50, and deprecated for Release 1.51. Most of the
functionality in Bio.SwissProt.SProt is available from Bio.SwissProt. Bio.SeqIO
currently uses Bio.SwissProt instead of Bio.SwissProt.SProt to parse SwissProt
files.
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, 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
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, 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
(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, 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.indexed_dict()
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, 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, 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.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.
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