[Biopython-announce] Biopython 1.30 release

Brad Chapman chapmanb at uga.edu
Fri May 14 10:34:30 EDT 2004

Hello all;
I'm happy to announce a new release of Biopython 1.30, available
today from http://biopython.org. This release contains a number of
new modules and substantial changes to older modules. As a result of
the changes, we've bumped up to a brand new major number. Please do
download, test with your code, and report any bugs or problems to
the normal lists (biopython at biopython.org or
biopython-dev at biopython.org). The substantial changes in this
release include:

-> Overhaul of the FASTA parser. Internally, fasta parsing now uses
C libraries, so it is much faster and scalable to large files. The
changes should all be internal, so that code written for the old
Fasta parser will work with the new version.

-> Updated GenBank parser internals. In a desire to make GenBank
parsing more flexible to the numerous updates to the format, a
number of underlying parser details have been improved.

-> New contributed modules:
   Affymetrix cel parsing -- Harry Zuzan
   Compass output parsing -- James Casbon
   Melting temperature calculation -- Sebastian Bassi
   Reduced protein alphabets -- Iddo Friedberg
   Blast XML output parsing -- Bertrand Frottier

-> Some duplicated and non-finished modules have been deprecated.
For now you will get DeprecationWarnings with these modules, but
they will eventually be removed. The effected modules are
Bio/sequtils, Bio/kMeans, Bio/SVM and Bio/RecordFile. Please see the
file DEPRECATED in the distribution for details of switching your
code to use the new replacement modules.

-> The C++ code in the KDTree and Affy modules is now compiled by
default. This has been tested on a number of platforms, but is a
potential source of compilation errors. If you run into any problems
compiling these C++ modules, please report them to the list.

-> A large assortment of bug fixes and updates to documentation.

A full list of changes is included below. Please download, test,
and enjoy. Thanks much for everyone's hard work that went into 
making this release possible.


May 14, 2004: Biopython 1.30
 Affy package added for dealing with Affymetrix cel files -- thanks to Harry 
 Added code for parsing Blast XML output -- thanks to Bertrand Frottier.
 Added code for parsing Compass output -- thanks to James Casbon.
 New melting temperature calculation module -- thanks to Sebastian Bassi.
 Added lowess function for non-parameteric regression -- thanks to Michiel.
 Reduced protein alphabet supported added -- thanks to Iddo.
 Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel
  and Thomas.
 Documentation added for converting between file formats.
 Updates to install documentation for non-root users -- thanks to Jakob 
 epydoc now used for automatic generation of documentation.

 Fasta parser updated to use Martel for parsing and indexing, allowing better
  speed and dealing with large data files.
 Updated to Registry code. Now 'from Bio import db' gives you a number of new
  retrieval options, including embl, fasta, genbak, interpro, prodoc and swissprot.
 GenBank parser uses new Martel format. GenBank retrieval now uses EUtils instead
  of the old non-working entrez scripts. GenBank indexing uses standard Mindy
  indexing. Fix for valueless qualifiers in feature keys -- thanks to Leighton 
 Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers
  -- thanks to Kristian Rother.
 Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard.

 Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo.
 Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso.
 PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon.
 Fix to NCBIWWW retrieval so that HTML results are returned correctly.
 Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh 
 Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to
  Ashleigh Smythe.
 Fixes to the Enyzme module -- thanks to Marc Colosimo.
 Fix for bugs in SeqUtils -- thanks to Frank Kauff.
 Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko.
 Fix to Fasta parsing to allow # comment lines -- thanks to Karl Diedrich.
 Updates to the C clustering library -- thanks to Michiel.
 Fixes for breakage in the SCOP module and addition of regression tests to
  framework -- thanks to Gavin.
 Various fixes to Bio.Wise -- thanks to Michael.
 Fix for bug in FastaReader -- thanks to Micheal.
 Fix EUtils bug where efetch would only return 500 sequences.
 Updates for Emboss commandlines, water and tranalign.
 Fixes to the FormatIO system of file conversion.

 C++ code (KDTree, Affy) now compiled by default on most platforms -- thanks to
  Michael for some nice distutils hacks and many people for testing.
 Deprecated Bio.sequtils -- use Bio.SeqUtils instead.
 Deprecated Bio.SVM -- use libsvm instead.
 Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead.
 Deprecated RecordFile -- doesn't appear to be finished code.

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