[Biopython-announce] Biopython 1.48 released

Michiel de Hoon mjldehoon at yahoo.com
Wed Sep 10 14:14:49 UTC 2008

We are pleased to announce the release of Biopython 1.48. Some new
functionality has been added, a few bugs have been fixed, the
documentation has been updated, plus several obsolete modules have
been deprecated (or explicitly labelled as obsolete).

The following additional file formats are now supported in Bio.SeqIO
and Bio.AlignIO:
    * reading and writing "tab" format (simple tab separated)
    * writing "nexus" files
    * reading "pir" files (NBRF/PIR)
    * basic support for writing "genbank" files (GenBank plain text)
This release also fixes some problems reading Clustal alignments
(introduced in Biopython 1.46 when consolidating Bio.AlignIO and
Bio.Clustalw), and some updates to the Bio.Sequencing parsers.

The SeqRecord and Alignment objects have a new method to get the
object as a string in a given file format (handled via Bio.SeqIO and

Bio.PubMed and the online code in Bio.GenBank are now considered
obsolete, and we intend to deprecate them after the next release. For
accessing PubMed and GenBank, please use Bio.Entrez instead.  Martel
and Bio.Mindy are now considered to be obsolete, and are likely to be
deprecated and removed in a future release, at which point we will
drop the optional dependency on mxTextTools.  Bio.Fasta is also
considered to be obsolete, please use Bio.SeqIO instead. We do intend
to deprecate this module eventually, however, for several years this
was the primary FASTA parsing module in Biopython and is likely to be
in use in many existing scripts.

In addition a number of other modules have been deprecated, including:
Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics -
see the DEPRECATED file for full details.

Source distributions are available from the Biopython website at
http://biopython.org, and Windows installers will be added shortly.

My thanks to all bug reporters, code contributors and others who made
this new release possible.

Peter, on behalf of the Biopython developers

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