Pin biopython to latest version 1.82

[pyup-bot]

This PR pins biopython to the latest release 1.82.

Changelog

1.51

the OBF mailing lists with EMBOSS, BioPerl, BioJava and BioRuby for inter-
conversion and the valid score range for each FASTQ variant. This means
Solexa FASTQ scores can be from -5 to 62 (format name "fastq-solexa" in
Bio.SeqIO), Illumina 1.3+ FASTQ files have PHRED scores from 0 to 62 (format
name "fastq-illumina"), and Sanger FASTQ files have PHRED scores from 0 to
93 (format name "fastq" or "fastq-sanger").

Bio.Sequencing.Phd has been updated, for example to cope with missing peak
positions. The "phd" support in Bio.SeqIO has also been updated to record
the PHRED qualities (and peak positions) in the SeqRecord's per-letter
annotation. This allows conversion of PHD files into FASTQ or QUAL which may
be useful for meta-assembly.

See the notes below for the Biopython 1.50 beta release for changes since
Biopython 1.49 was released. This includes dropping support for Python 2.3,
removing our deprecated parsing infrastructure (Martel and Bio.Mindy), and
hence removing any dependence on mxTextTools.

Additionally, since the beta, a number of small bugs have been fixed, and
there have been further additions to the test suite and documentation.


June 23, 2009: Biopython 1.51 beta released.
============================================

Biopython no longer supports Python 2.3.  Currently we support Python 2.4,
2.5 and 2.6.

Our deprecated parsing infrastructure (Martel and Bio.Mindy) has been
removed.  This means Biopython no longer has any dependence on mxTextTools.

A few cosmetic issues in GenomeDiagram with arrow sigils and labels on
circular diagrams have been fixed.

Bio.SeqIO will now write GenBank files with the feature table (previously
omitted), and a couple of obscure errors parsing ambiguous locations have
been fixed.

Bio.SeqIO can now read and write Illumina 1.3+ style FASTQ files (which use
PHRED quality scores with an ASCII offset of 64) under the format name
"fastq-illumina". Biopython 1.50 supported just "fastq" (the original Sanger
style FASTQ files using PHRED scores with an ASCII offset of 33), and
"fastq-solexa" (the original Solexa/Illumina FASTQ format variant holding
Solexa scores with an ASCII offset of 64) .

For parsing the "swiss" format, Bio.SeqIO now uses the new Bio.SwissProt
parser, making it about twice as fast as in Biopython 1.50, where the older
now deprecated Bio.SwissProt.SProt was used. There should be no functional
differences as a result of this change.

Our command line wrapper objects have been updated to support accessing
parameters via python properties, and setting of parameters at initiation
with keyword arguments.  Additionally Cymon Cox has contributed several new
multiple alignment wrappers under Bio.Align.Applications.

A few more issues with Biopython's BioSQL support have been fixed (mostly by
Cymon Cox). In particular, the default PostgreSQL schema includes some rules
intended for BioPerl support only, which were causing problems in Biopython
(see BioSQL bug 2839).

There have also been additions to the tutorial, such as the new alignment
wrappers, with a whole chapter for the SeqRecord object. We have also added
to the unit test coverage.


April 20, 2009: Biopython 1.50 released.
========================================

See the notes below for the Biopython 1.50 beta release for more details,
but the highlights are:

* The SeqRecord supports slicing and per-letter-annotation
* Bio.SeqIO can read and write FASTQ and QUAL files
* Bio.Seq now has an UnknownSeq object
* GenomeDiagram has been integrated into Biopython
* New module Bio.Motif will later replace Bio.AlignAce and Bio.MEME
* This will be the final release to support Python 2.3
* This will be the final release with Martel and Bio.Mindy

Since the 1.50 beta release:

* The NCBI's Entrez EFetch no longer supports rettype="genbank"
and "gb" (or "gp") should be used instead.
* Bio.SeqIO now supports "gb" as an alias for "genbank".
* The Seq object now has string-like startswith and endswith methods
* Bio.Blast.NCBIXML now has a read function for single record files
* A few more unit tests were added
* More documentation


April 3, 2009: Biopython 1.50 beta released.
============================================

The SeqRecord object has a new dictionary attribute, letter_annotations,
which is for holding per-letter-annotation information like sequence
quality scores or secondary structure predictions.  As part of this work,
the SeqRecord object can now be sliced to give a new SeqRecord covering
just part of the sequence.  This will slice the per-letter-annotation to
match, and will also include any SeqFeature objects as appropriate.

Bio.SeqIO can now read and write FASTQ and QUAL quality files using PHRED
quality scores (Sanger style, also used for Roche 454 sequencing), and FASTQ
files using Solexa/Illumina quality scores.

The Bio.Seq module now has an UnknownSeq object, used for when we have a
sequence of known length, but unknown content.  This is used in parsing
GenBank and EMBL files where the sequence may not be present (e.g. for a
contig record) and when parsing QUAL files (which don't have the sequence)

GenomeDiagram by Leighton Pritchard has been integrated into Biopython as
the Bio.Graphics.GenomeDiagram module  If you use this code, please cite the
publication Pritchard et al. (2006), Bioinformatics 22 616-617.  Note that
like Bio.Graphics, this requires the ReportLab python library.

A new module Bio.Motif has been added, which is intended to replace the
existing Bio.AlignAce and Bio.MEME modules.

The set of NCBI DTD files included with Bio.Entrez has been updated with the
revised files the NCBI introduced on 1 Jan 2009.

Minor fix to BioSQL for retrieving references and comments.

Bio.SwissProt has a new faster parser which will be replacing the older
slower code in Bio.SwissProt.SProt (which we expect to deprecate in the next
release).

We've also made some changes to our test framework, which is now given a
whole chapter in the tutorial.  This intended to help new developers or
contributors wanting to improve our unit test coverage.


November 21, 2008: Biopython 1.49 released.
===========================================

See the notes below for the Biopython 1.49 beta release for more details,
but the highlights are:

* Biopython has transitioned from Numeric to NumPy
* Martel and Bio.Mindy are now deprecated

Since the 1.49 beta release:

* A couple of NumPy issues have been resolved
* Further small improvements to BioSQL
* Bio.PopGen.SimCoal should now work on Windows
* A few more unit tests were added


November 7, 2008: Biopython 1.49 beta released.
===============================================

Biopython has transitioned from Numeric to NumPy.  Please move to NumPy.

A number of small changes have been made to support Python 2.6 (mostly
avoiding deprecated functionality), and further small changes have been
made for better compatibility with Python 3 (this work is still ongoing).
However, we intend to support Python 2.3 for only a couple more releases.

As part of the Numeric to NumPy migration, Bio.KDTree has been rewritten in
C instead of C++ which therefore simplifies building Biopython from source.

Martel and Bio.Mindy are now considered to be deprecated, meaning mxTextTools
is no longer required to use Biopython.  See the DEPRECATED file for details
of other deprecations.

The Seq object now supports more string like methods (gaining find, rfind,
split, rsplit, strip, lstrip and rstrip in addition to previously supported
methods like count).  Also, biological methods transcribe, back_transcribe
and translate have been added, joining the pre-existing reverse_complement
and complement methods.  Together these changes allow a more object
orientated programming style using the Seq object.

The behaviour of the Bio.Seq module's translate function has changed so that
ambiguous codons which could be a stop codon like "TAN" or "NNN" are now
translated as "X" (consistent with EMBOSS and BioPerl - Biopython previously
raised an exception), and a bug was fixed so that invalid codons (like "A-T")
now raise an exception (previously these were translated as stop codons).

BioSQL had a few bugs fixed, and can now optionally fetch the NCBI taxonomy
on demand when loading sequences (via Bio.Entrez) allowing you to populate
the taxon/taxon_name tables gradually.  This has been tested in combination
with the BioSQL load_ncbi_taxonomy.pl script used to populate or update the
taxon/taxon_name tables.  BioSQL should also now work with the psycopg2
driver for PostgreSQL as well as the older psycopg driver.

The PDB and PopGen sections of the Tutorial have been promoted to full
chapters, and a new chapter has been added on supervised learning methods
like logistic regression.  The "Cookbook" section now has a few graphical
examples using Biopython to calculate sequence properties, and matplotlib
(pylab) to plot them.

The input functions in Bio.SeqIO and Bio.AlignIO now accept an optional
argument to specify the expected sequence alphabet.

The somewhat quirky unit test GUI has been removed, the unit tests are now
run via the command line by default.


September 8, 2008: Biopython 1.48 released.
===========================================

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

Additional file formats 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)

Fixed some problems reading Clustal alignments (introduced in Biopython 1.46
when consolidating Bio.AlignIO and Bio.Clustalw).

Updates to the Bio.Sequencing parsers.

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.

Bio.Fasta is now 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.

Martel and Bio.Mindy are now considered to be obsolete, and are likely to be
deprecated and removed in a future release.

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.


July 5, 2008: Biopython 1.47 released.
======================================

Improved handling of ambiguous nucleotides in Bio.Seq.Translate().
Better handling of stop codons in the alphabet from a translation.
Fixed some codon tables (problem introduced in Biopython 1.46).

Updated Nexus file handling.

Fixed a bug in Bio.Cluster potentially causing segfaults in the
single-linkage hierarchical clustering library.

Added some DTDs to be able to parse EFetch results from the
nucleotide database.

Added IntelliGenetics/MASE parsing to Bio.SeqIO (as the "ig" format).


June 29, 2008: Biopython 1.46 released.
=======================================

Bio.Entrez now has several Entrez format XML parsers, and a chapter
in the tutorial.

Addition of new Bio.AlignIO module for working with sequence alignments
in the style introduced with Bio.SeqIO in recent releases, with a whole
chapter in the tutorial.

A problem parsing certain EMBL files was fixed.

Several minor fixes were made to the NCBI BLAST XML parser, including
support for the online version 2.2.18+ introduced in May 2008.

The NCBIWWW.qblast() function now allows other programs (blastx, tblastn,
tblastx) in addition to just blastn and blastp.

Bio.EUtils has been updated to explicitly enforce the NCBI's rule of at
most one query every 3 seconds, rather than assuming the user would obey
this.

Iterators in Bio.Medline, Bio.SCOP, Bio.Prosite, Bio.Prosite.Prodoc,
Bio.SwissProt, and others to make them more generally usable.

Phylip export added to Bio.Nexus.

Improved handling of ambiguous nucleotides and stop codons in
Bio.Seq.Translate (plus introduced a regression fixed in Biopython 1.47).


March 22, 2008: Biopython 1.45 released.
========================================

The Seq and MutableSeq objects act more like python strings, in particular
str(object) now returns the full sequence as a plain string.  The existing
tostring() method is preserved for backwards compatibility.

BioSQL has had some bugs fixed, and has an additional unit test which loads
records into a database using Bio.SeqIO and then checks the records can be
retrieved correctly.  The DBSeq and DBSeqRecord classes now subclass the
Seq and SeqRecord classes, which provides more functionality.

The modules under Bio.WWW are being deprecated.
Functionality in Bio.WWW.NCBI, Bio.WWW.SCOP, Bio.WWW.InterPro and
Bio.WWW.ExPASy is now available from Bio.Entrez, Bio.SCOP, Bio.InterPro and
Bio.ExPASy instead. Bio.Entrez was used to fix a nasty bug in Bio.GenBank.

Tiago Antao has included more functionality in the Population Genetics
module, Bio.PopGen.

The Bio.Cluster module has been updated to be more consistent with other
Biopython code.

The tutorial has been updated, including devoting a whole chapter to
Swiss-Prot, Prosite, Prodoc, and ExPASy. There is also a new chapter on
Bio.Entrez.

Bio.biblio was deprecated.


October 28, 2007: Biopython 1.44 released.
==========================================

NOTE: This release includes some rather drastic code changes, which were
necessary to get Biopython to work with the new release of mxTextTools.

The (reverse)complement functions in Bio.Seq support ambiguous nucleotides.

Bio.Kabat, which was previously deprecated, is now removed from Biopython.

Bio.MarkupEditor was deprecated, as it does not appear to have any users.

Bio.Blast.NCBI.qblast() updated with more URL options, thanks to a patch
from Chang Soon Ong.

Several fixes to the Blast parser.

The deprecated Bio.Blast.NCBIWWW functions blast and blasturl were removed.

The standalone Blast functions blastall, blastpgp now create XML output by
default.

Bio.SeqIO.FASTA and Bio.SeqIO.generic have been deprecated in favour of
the new Bio.SeqIO module.

Bio.FormatIO has been removed (a gradual deprecation was not possible).
Please look at Bio.SeqIO for sequence input/output instead.

Fix for a bug in Bio.Cluster, which caused kcluster() to hang on some
platforms.

Bio.expressions has been deprecated.

Bio.SeqUtils.CheckSum created, including new methods from Sebastian Bassi,
and functions crc32 and crc64 which were moved from Bio/crc.py.
Bio.crc is now deprecated. Bio.lcc was updated and moved to Bio.SeqUtils.lcc.

Bio.SwissProt parser updated to cope with recent file format updates.

Bio.Fasta, Bio.KEGG and Bio.Geo updated to pure python parsers which
don't rely on Martel.

Numerous fixes in the Genbank parser.

Several fixes in Bio.Nexus.

Bio.MultiProc and Bio.Medline.NLMMedlineXML were deprecating, as they failed
on some platforms, and seemed to have no users. Deprecated concurrent
behavior in Bio.config.DBRegistry and timeouts in Bio.dbdefs.swissprot,
which relies on Bio.MultiProc.

Tiago Antao has started work on a Population Genetics module, Bio.PopGen

Updates to the tutorial, including giving Bio.Seq and Bio.SeqIO a whole
chapter each.


March 17, 2007: Biopython 1.43 released.
========================================

New Bio.SeqIO module for reading and writing biological sequence files
in various formats, based on SeqRecord objects.  This includes a new fasta
parser which is much faster than Bio.Fasta, particularly for larger files.
Easier to use, too.

Various improvements in Bio.SeqRecord.

Running Blast using Bio.Blast.NCBIStandalone now generates output in XML
format by default.
The new function Bio.Blast.NCBIXML.parse can parse multiple Blast records
in XML format.

Bio.Cluster no longer uses ranlib, but uses its own random number generator
instead. Some modifications to make Bio.Cluster more compatible with the new
NumPy (we're not quite there yet though).

New Bio.UniGene parser.

Numerous improvements in Bio.PDB.

Bug fixes in Bio.SwissProt, BioSQL, Bio.Nexus, and other modules.

Faster parsing of large GenBank files.

New EMBL parser under Bio.GenBank and also integrated into (new) Bio.SeqIO

Compilation of KDTree (C++ code) is optional (setup.py asks the user if it
should be compiled). For the Windows installer, C++ code is now included.

Nominating Bio.Kabat for removal.

Believe it or not, even the documentation was updated.


July 16, 2006: Biopython 1.42 released.
=======================================

Bio.GenBank: New parser by Peter, which doesn't rely on Martel.

Numerous updates in Bio.Nexus and Bio.Geo.

Bio.Cluster became (somewhat) object-oriented.

Lots of bug fixes, and updates to the documentation.


October 28, 2005: Biopython 1.41 released.
==========================================

Major changes:

NEW: Bio.MEME -- thanks to Jason Hackney

Added transcribe, translate, and reverse_complement functions to Bio.Seq that
work both on Seq objects and plain strings.

Major code optimization in cpairwise2module.

CompareACE support added to AlignAce.

Updates to Blast parsers in Bio.Blast, in particular use of the XML parser
in NCBIXML contributed by Bertrand Frottier, and the BLAT parser by Yair
Benita.

Pairwise single-linkage hierarchical clustering in Bio.Cluster became much
faster and memory-efficient, allowing clustering of large data sets.

Bio.Emboss: Added command lines for einverted and palindrome.

Bio.Nexus: Added support for StringIO objects.

Numerous updates in Bio.PDB.

Lots of fixes in the documentation.

March 29, 2005: MEME parser added. Thanks to Jason Hackney


Feb 18, 2005: Biopython 1.40 beta
=================================
Major Changes since v1.30. For a full list of changes please see the CVS

IMPORTANT: Biopython now works with Python version >= 2.3

NEW: Bio.Nexus -- thanks to Frank Kauff
Bio.Nexus is a Nexus file parser. Nexus is a common format for phylogenetic
trees.

NEW: CAPS module -- Thanks to Jonathan Taylor.

NEW: Restriction enzyme package contributed by Frederic Sohm. This includes
classes for manipulating enzymes, updating from Rebase, as well as
documentation and Tests.

CHANGED: Bio.PDB -- thanks to Thomas Hamelryck.

- Added atom serial number.
- Epydoc style documentation.
- Added secondary structure support (through DSSP).
- Added Accessible Surface Area support (through DSSP).
- Added Residue Depth support (through MSMS).
- Added Half Sphere Exposure.
- Added Fragment classification of the protein backbone (see Kolodny et al.,
- JMB, 2002).
- Corrected problem on Windows with PDBList (thanks to Matt Dimmic)
- Added StructureAlignment module to superimpose structures based on a FASTA
sequence alignment.
- Various additions to Polypeptide.
- Various bug corrections in Vector.
- Lots of smaller bug corrections and additional features

CHANGED: MutableSeq -- thanks to Michiel De Hoon
Added the functions 'complement' and 'reverse_complement' to Bio.Seq's Seq and
MutableSeq objects. Similar functions previously existed in various locations
in BioPython:

- forward_complement, reverse_complement in Bio.GFF.easy
- complement, antiparallel in Bio.SeqUtils

These functions have now been deprecated, and will issue a DeprecationWarning
when used. The functions complement and reverse_complement, when applied to a
Seq object, will return a new Seq object. The same function applied to a
MutableSeq object will modify the MutableSeq object itself, and don't return
anything.


May 14, 2004: Biopython 1.30
============================

- Affy package added for dealing with Affymetrix cel files -- thanks to Harry
Zuzan.
- 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
Fredslund.
- 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 Pritchard.
- 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
Smythe.
- 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.


Feb 16, 2004: Biopython 1.24
============================

- New parsers for Phred and Ace format files -- thanks to Frank Kauff
- New Code for dealing with NMR data -- thanks to Bob Bussell
- New SeqUtils modules for codon usage, isoelectric points and other
protein properties -- thanks to Yair Benita
- New code for dealing with Wise contributed by Michael
- EZ-Retrieve sequence retrieval now supported thanks to Jeff
- Bio.Cluster updated along with documentation by Michiel
- BioSQL fixed so it now works with the current SQL schema -- thanks to Yves
Bastide for patches
- Patches to Bio/__init__ to make it compatible with py2exe -- thanks to
Leighton Pritchard
- Added __iter__ to all Biopython Iterators to make them Python 2.2 compatible
- Fixes to NCBIWWW for retrieving from NCBI -- thanks to Chris Wroe
- Retrieval of multiple alignment objects from BLAST records -- thanks to
James Casbon
- Fixes to GenBank format for new tags by Peter
- Parsing fixes in clustalw parsed -- thanks to Greg Singer and Iddo
- Fasta Indexes can have a specified filename -- thanks to Chunlei Wu
- Fix to Prosite parser -- thanks to Mike Liang
- Fix in GenBank parsing -- mRNAs now get strand information


Oct 18, 2003: Biopython 1.23
============================

- Fixed distribution of files in Bio/Cluster
- Now distributing Bio/KDTree/_KDTree.swig.C
- minor updates in installation code
- added mmCIF support for PDB files


Oct 9, 2003: Biopython 1.22
===========================

- Added Peter Slicker's patches for speeding up modules under Python 2.3
- Fixed Martel installation.
- Does not install Bio.Cluster without Numeric.
- Distribute EUtils DTDs.
- Yves Bastide patched NCBIStandalone.Iterator to be Python 2.0 iterator
- Ashleigh's string coercion fixes in Clustalw.
- Yair Benita added precision to the protein molecular weights.
- Bartek updated AlignAce.Parser and added Motif.sim method
- bug fixes in Michiel De Hoon's clustering library
- Iddo's bug fixes to Bio.Enzyme and new RecordConsumer
- Guido Draheim added patches for fixing import path to xbb scripts
- regression tests updated to be Python 2.3 compatible
- GenBank.NCBIDictionary is smarter about guessing the format


Jul 28, 2003: Biopython 1.21
============================

- Martel added back into the released package
- new AlignACE module by Bartek Wilczynski
- Andreas Kuntzagk fix for GenBank Iterator on empty files


Jul 27, 2003: Biopython 1.20
============================

- added Andrew Dalke's EUtils library
- added Michiel de Hoon's gene expression analysis package
- updates to setup code, now smarter about dependencies
- updates to test suite, now smarter about code that is imported
- Michael Hoffman's fixes to DocSQL
- syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible
- updates in NCBIStandalone, short query error
- Sebastian Bassi submitted code to calculate LCC complexity
- Greg Kettler's NCBIStandalone fix for long query lengths
- slew of miscellaneous fixes from George Paci
- miscellaneous cleanups and updates from Andreas Kuntzagk
- Peter Bienstman's fixes to Genbank code -- now parses whole database
- Kayte Lindner's LocusLink package
- miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman
- miscellaneous BLAST fixes and updates
- Iddo added new code to parse BLAST table output format
- Karl Diedrich's patch to read T_Coffee files
- Larry Heisler's fix for primer3 output
- Bio.Medline now uses proper iterator objects
- copen now handles SIGTERM correctly
- small bugfixes and updates in Thomas Hamelryck's PDB package
- bugfixes and updates to SeqIO.FASTA reader
- updates to Registry system, conforms to 2003 hackathon OBDA spec
- Yu Huang patch to support tblastn in wublast expression


Dec 17, 2002: Biopython 1.10
============================

- Python requirement bumped up to 2.2
- hierarchy reorg, many things moved upwards into Bio namespace
- pairwise2 replaces fastpairwise and pairwise
- removed deprecated Sequence.py package
- minor bug fix in File.SGMLStripper
- added Scripts/debug/debug_blast_parser.py to diagnose blast parsing errors
- IPI supported by SwissProt/SProt.py parser
- large speedup for kmeans
- new registry framework for generic access to databases and parsers
- small bug fix in stringfns.split
- scripts that access NCBI moved over to new EUtils system
- new crc module
- biblio.py supports the EBI Bibliographic database
- new CDD parser
- new Ndb parser
- new ECell parser
- new Geo parser
- access to GFF databases
- new KDTree data structure
- new LocusLink parser
- new MarkovModel algorithm
- new Saf parser
- miscellaneous sequence handling functions in sequtils
- new SVDSuperimpose algorithm

1.2

files can be downloaded from the EBI ftp site:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Damien Goutte-Gattat
- Gert Hulselmans
- João Rodrigues
- Markus Piotrowski
- Pascal Schläpfer (first contribution)
- Leighton Pritchard
- Sergio Valqui
- Suyash Gupta
- Vini Salazar (first contribution)


4 September 2020: Biopython 1.78
================================

This release of Biopython supports Python 3.6, 3.7 and 3.8. It has also been
tested on PyPy3.6.1 v7.1.1.

The main change is that ``Bio.Alphabet`` is no longer used. In some cases you
will now have to specify expected letters, molecule type (DNA, RNA, protein),
or gap character explicitly. Please consult the updated Tutorial and API
documentation for guidance. This simplification has sped up many ``Seq``
object methods. See https://biopython.org/wiki/Alphabet for more information.

``Bio.SeqIO.parse()`` is faster with "fastq" format due to small improvements
in the ``Bio.SeqIO.QualityIO`` module.

The ``SeqFeature`` object's ``.extract()`` method can now be used for
trans-spliced locations via an optional dictionary of references.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with additions
to the test suite. There has been further work to follow the Python PEP8,
PEP257 and best practice standard coding style, and all of the tests have
been reformatted with the ``black`` tool to match the main code base.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Adam Sjøgren (first contribution)
- Carlos Pena
- Chris Daley
- Chris Rands
- Christian Brueffer
- Damien Goutte-Gattat
- João Rodrigues
- João Vitor F Cavalcante (first contribution)
- Marie Crane
- Markus Piotrowski
- Michiel de Hoon
- Peter Cock
- Sergio Valqui
- Yogesh Kulkarni (first contribution)
- Zheng Ruan

25 May 2020: Biopython 1.77
===========================

This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been
tested on PyPy3.6.1 v7.1.1-beta0.

**We have dropped support for Python 2 now.**

``pairwise2`` now allows the input of parameters with keywords and returns the
alignments as a list of ``namedtuples``.

The codon tables have been updated to NCBI genetic code table version 4.5,
which adds Cephalodiscidae mitochondrial as table 33.

Updated ``Bio.Restriction`` to the January 2020 release of REBASE.

A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
handle protein structure transformations using dihedral angles (internal
coordinates). The new framework supports lossless interconversion between
internal and cartesian coordinates, which, among other uses, simplifies the
analysis and manipulation of coordinates of proteins structures.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and all the main code
base has been reformatted with the ``black`` tool.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Alexander Decurnou (first contribution)
- Andrei Istrate (first contribution)
- Andrey Raspopov
- Artemi Bendandi (first contribution)
- Austin Varela (first contribution)
- Chris Daley
- Chris Rands
- Deepak Khatri
- Hielke Walinga (first contribution)
- Kai Blin
- Karthikeyan Singaravelan (first contribution)
- Konstantinos Zisis (first contribution)
- Markus Piotrowski
- Michiel de Hoon
- Peter Cock
- Rob Miller
- Sergio Valqui
- Steve Bond
- Sujan Dulal (first contribution)
- Tianyi Shi (first contribution)

20 December 2019: Biopython 1.76
================================

This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has
also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.

We intend this to be our final release supporting Python 2.7 and 3.5.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.


``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
output.

In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
CPUs under Linux thanks to Travis CI. Further post-release testing done by
Debian and other packagers and distributors of Biopython also covers these
CPUs.

``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
re-written: it now applies ``.calculate()`` to chunks of the sequence
to maintain a low memory footprint for long sequences.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite. There has been further work to follow the Python
PEP8, PEP257 and best practice standard coding style, and more of the code
style has been reformatted with the ``black`` tool.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Chris Daley (first contribution)
- Chris Rands
- Christian Brueffer
- Ilya Flyamer (first contribution)
- Jakub Lipinski (first contribution)
- Michael R. Crusoe (first contribution)
- Michiel de Hoon
- Peter Cock
- Sergio Valqui

6 November 2019: Biopython 1.75
===============================

This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected
to work on the soon to be released Python 3.8. It has also been tested on
PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.

Note we intend to drop Python 2.7 support in early 2020.

The restriction enzyme list in ``Bio.Restriction`` has been updated to the
August 2019 release of REBASE.

``Bio.SeqIO`` now supports reading and writing files in the native format of
Christian Marck's DNA Strider program ("xdna" format, also used by Serial
Cloner), as well as reading files in the native formats of GSL Biotech's
SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").

``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
format (work funded by the National Marrow Donor Program).

The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.

The ``MMTFIO`` class has been added that allows writing of MMTF file format
files from a Biopython structure object. ``MMTFIO`` has a similar interface to
``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
out a specified selection. This final addition to read/write support for
PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.

Values from mmCIF files are now read in as a list even when they consist of a
single value. This change improves consistency and reduces the likelihood of
making an error, but will require user code to be updated accordingly.

`Bio.motifs.meme` has been updated to parse XML output files from MEME over
the plain-text output file. The goal of this change is to parse a more
structured data source with minimal loss of functionality upon future MEME
releases.

``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
PDB-style Astral files.

A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
pretty print method ``format_alignment`` to restore the output of local
alignments to the 'old' format (showing the whole sequences including the
un-aligned parts instead of only showing the aligned parts).

A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
``IsoelectricPoint`` in ``Bio.SeqUtils``.

The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
pairwise alignments, i.e. alignments of any Python object, for example
three-letter amino acid sequences, three-nucleotide codons, and arrays of
integers.

A new module ``substitution_matrices`` was added to ``Bio.Align``, which
includes an ``Array`` class that can be used as a substitution matrix. As
the ``Array`` class is a subclass of a numpy array, mathematical operations
can be applied to it directly, and C code that makes use of substitution
matrices can directly access the numerical values stored in the substitution
matrices. This module is intended as a replacement of ``Bio.SubsMat``,
which is currently unmaintained.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style. We have also
started to use the ``black`` Python code formatting tool.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Chris MacRaild
- Chris Rands
- Damien Goutte-Gattat (first contribution)
- Devang Thakkar
- Harry Jubb
- Joe Greener
- Kiran Mukhyala (first contribution)
- Konstantin Vdovkin
- Mark Amery
- Markus Piotrowski
- Michiel de Hoon
- Mike Moritz (first contribution)
- Mustafa Anil Tuncel
- Nick Negretti
- Osvaldo Zagordi (first contribution)
- Peter Cock
- Peter Kerpedjiev
- Sergio Valqui
- Spencer Bliven
- Victor Lin


16 July 2019: Biopython 1.74
============================

This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However,
it will be the last release to support Python 3.4 which is now at end-of-life.
It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now
have a string-like ``.join()`` method.

The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning
the fields may not always follow the historical column based positions. We
no longer give a warning when parsing these. We now allow writing such files
(although with a warning as support for reading them is not yet widespread).

Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added.

We now capture the IDcode field from PDB Header records.

``Bio.pairwise2``'s pretty-print output from ``format_alignment`` has been
optimized for local alignments: If they do not consist of the whole sequences,
only the aligned section of the sequences are shown, together with the start
positions of the sequences (in 1-based notation). Alignments of lists will now
also be prettily printed.

``Bio.SearchIO`` now supports parsing the text output of the HHsuite protein
sequence search tool. The format name is ``hhsuite2-text`` and
``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively.

``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``. This
attribute is meant for capturing the order by which the HSP were output in the
parsed file and is set with a default value of -1 for all HSP objects. It is
also used for sorting the output of ``QueryResult.hsps``.

``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing. The
goal of this change is make the parser more robust by being able to extract
string-values that are not utf-8-encoded. This affects all tag values, except
for ID and description values, where they need to be extracted as strings
to conform to the ``SeqRecord`` interface. In this case, the parser will
attempt to decode using ``utf-8`` and fall back to the system encoding if that
fails. This change affects Python 3 only.

``Bio.motifs.mast`` has been updated to parse XML output files from MAST over
the plain-text output file. The goal of this change is to parse a more
structured data source with minimal loss of functionality upon future MAST
releases. Class structure remains the same plus an additional attribute
``Record.strand_handling`` required for diagram parsing.

``Bio.Entrez`` now automatically retries HTTP requests on failure. The
maximum number of tries and the sleep between them can be configured by
changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.
(The defaults are 3 tries and 15 seconds, respectively.)

The restriction enzyme list in ``Bio.Restriction`` has been updated to the May
2019 release of REBASE.

All tests using the older print-and-compare approach have been replaced by
unittests following Python's standard testing framework.

On the documentation side, all the public modules, classes, methods and
functions now have docstrings (built in help strings). Furthermore, the PDF
version of the *Biopython Tutorial and Cookbook* now uses syntax coloring
for code snippets.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Andrey Raspopov (first contribution)
- Antony Lee
- Benjamin Rowell (first contribution)
- Bernhard Thiel
- Brandon Invergo
- Catherine Lesuisse
- Chris Rands
- Deepak Khatri (first contribution)
- Gert Hulselmans
- Jared Andrews
- Jens Thomas (first contribution)
- Konstantin Vdovkin
- Lenna Peterson
- Mark Amery
- Markus Piotrowski
- Micky Yun Chan (first contribution)
- Nick Negretti
- Peter Cock
- Peter Kerpedjiev
- Ralf Stephan
- Rob Miller (first contribution)
- Sergio Valqui
- Victor Lin
- Wibowo 'Bow' Arindrarto
- Zheng Ruan


18 December 2018: Biopython 1.73
================================

This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7.
It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

As in recent releases, more of our code is now explicitly available under
either our original "Biopython License Agreement", or the very similar but
more commonly used "3-Clause BSD License".  See the ``LICENSE.rst`` file for
more details.

The dictionary-like indexing in SeqIO and SearchIO will now explicitly preserve
record order to match a behaviour change in the Python standard dict object.
This means looping over the index will load the records in the on-disk order,
which will be much faster (previously it would be effectively at random, based
on the key hash sorting).

The "grant" matrix in Bio.SubsMat.MatrixInfo has been replaced as our original
values taken from Gerhard Vogt's old webpages at EMBL Heidelberg were
discovered to be in error. The new values have been transformed following
Vogt's approach, taking the global maximum 215 minus the similarity scores
from the original paper Grantham (1974), to give a distance measure.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style.

Double-quote characters in GenBank feature qualifier values in ``Bio.SeqIO``
are now escaped as per the NCBI standard. Improperly escaped values trigger a
warning on parsing.

There is a new command line wrapper for the BWA-MEM sequence mapper.

The string-based FASTA parsers in ``Bio.SeqIO.FastaIO`` have been optimised,
which also speeds up parsing FASTA files using ``Bio.SeqIO.parse()``.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Alona Levy-Jurgenson (first contribution)
- Ariel Aptekmann
- Brandon Invergo
- Catherine Lesuisse
- Chris Rands
- Darcy Mason (first contribution)
- Devang Thakkar (first contribution)
- Ivan Antonov (first contribution)
- Jeremy LaBarage (first contribution)
- Juraj Szász (first contribution)
- Kai Blin
- Konstantin Vdovkin (first contribution)
- Manuel Nuno Melo (first contribution)
- Maximilian Greil
- Nick Negretti (first contribution)
- Peter Cock
- Rona Costello (first contribution)
- Spencer Bliven
- Wibowo 'Bow' Arindrarto
- Yi Hsiao (first contribution)


21 June 2018: Biopython 1.72
============================

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6.
It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
SeqIO.write (especially when used in a for loop).

The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
inclusive end coordinates to better handle searches at end points. This
will require you to rebuild any existing MAF index files.

In this release more of our code is now explicitly available under either our
original "Biopython License Agreement", or the very similar but more commonly
used "3-Clause BSD License".  See the ``LICENSE.rst`` file for more details.

The Entrez module now supports the NCBI API key. Also you can now set a custom
directory for DTD and XSD files. This allows Entrez to be used in environments
like AWS Lambda, which restricts write access to specific directories.
Improved support for parsing NCBI Entrez XML files that use XSD schemas.

Internal changes to our C code mean that NumPy is no longer required at
compile time - only at run time (and only for those modules which use NumPy).

Seq, UnknownSeq, MutableSeq and derived classes now support integer
multiplication methods, matching native Python string methods.

A translate method has been added to Bio.SeqFeature that will extract a
feature and translate it using the codon_start and transl_table qualifiers
of the feature if they are present.

Bio.SearchIO is no longer considered experimental, and so it does not raise
warnings anymore when imported.

A new pairwise sequence aligner is available in Bio.Align, as an alternative
to the existing pairwise sequence aligner in Bio.pairwise2.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Benjamin Vaisvil (first contribution)
- Blaise Li
- Chad Parmet
- Chris Rands
- Connor T. Skennerton
- Francesco Gastaldello
- Michiel de Hoon
- Pamela Russell (first contribution)
- Peter Cock
- Spencer Bliven
- Stefans Mezulis
- Wibowo 'Bow' Arindrarto


3 April 2018: Biopython 1.71
============================

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6.
It has also been tested on PyPy2.7 v5.10.0 and PyPy3.5 v5.10.1.

Python 3 is the primary development platform for Biopython. We will drop
support for Python 2.7 no later than 2020, in line with the end-of-life or
sunset date for Python 2.7 itself.

Encoding issues have been fixed in several parsers when reading data files
with non-ASCII characters, like accented letters in people's names. This would
raise ``UnicodeDecodeError: 'ascii' codec can't decode byte ...`` under some
system locale settings.

Bio.KEGG can now parse Gene files.

The multiple-sequence-alignment object used by Bio.AlignIO etc now supports
a per-column annotation dictionary, useful for richly annotated alignments
in the Stockholm/PFAM format.

The SeqRecord object now has a translate method, following the approach used
for its existing reverse_complement method etc.

The output of function ``format_alignment`` in ``Bio.pairwise2`` for displaying
a pairwise sequence alignment as text now indicates gaps and mis-matches.

Bio.SeqIO now supports reading and writing two-line-per-record FASTA files
under the format name "fasta-2line", useful if you wish to work without
line-wrapped sequences.

Bio.PDB now contains a writer for the mmCIF file format, which has been the
standard PDB archive format since 2014. This allows structural objects to be
written out and facilitates conversion between the PDB and mmCIF file formats.

Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc
wrapper and include a new wrapper for fuzzpro.

The restriction enzyme list in ``Bio.Restriction`` has been updated to the
November 2017 release of REBASE.

New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2)
were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain
no dedicated stop codons; the stop codons in these codes have a context
dependent encoding as either STOP or as amino acid.

IO functions such as ``SeqIO.parse`` now accept any objects which can be passed
to the builtin ``open`` function. Specifically, this allows using
``pathlib.Path`` objects under Python 3.6 and newer, as per `PEP 519
<https://www.python.org/dev/peps/pep-0519/>`_.

Bio.SearchIO can now parse InterProScan XML files.

For Python 3 compatibility, comparison operators for the entities within a
Bio.PDB Structure object were implemented. These allow the comparison of
models, chains, residues, and atoms with the common operators  (==, !=, >, ...)
Comparisons are based on IDs and take the parents of the entity up to the
model level into account. For consistent behaviour of all entities the
operators for atoms were modified to also consider the parent IDs. NOTE: this
represents a change in behaviour in respect to v1.70 for Atom comparisons. In
order to mimic the behaviour of previous versions, comparison will have to be
done for Atom IDs and alternative locations specifically.

In this release more of our code is now explicitly available under either our
original "Biopython License Agreement", or the very similar but more commonly
used "3-Clause BSD License".  See the ``LICENSE.rst`` file for more details.

Additionally, a number of small bugs and typos have been fixed with further
additions to the test suite, and there has been further work to follow the
Python PEP8, PEP257 and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Adhemar Zerlotini
- Ariel Aptekmann
- Chris Rands
- Christian Brueffer
- Connor T. Skennerton
- Erik Cederstrand (first contribution)
- Fei Qi (first contribution)
- Francesco Gastaldello
- James Jeffryes (first contribution)
- Jerven Bolleman (first contribution)
- Joe Greener (first contribution)
- Joerg Schaarschmidt (first contribution)
- João Rodrigues
- Jeroen Van Goey
- Jun Aruga (first contribution)
- Kai Blin
- Kozo Nishida
- Lewis A. Marshall (first contribution)
- Markus Piotrowski
- Michiel de Hoon
- Nicolas Fontrodona (first contribution)
- Peter Cock
- Philip Bergstrom (first contribution)
- rht (first contribution)
- Saket Choudhary
- Shuichiro MAKIGAKI (first contribution)
- Shyam Saladi (first contribution)
- Siong Kong
- Spencer Bliven
- Stefans Mezulis
- Steve Bond
- Yasar L. Ahmed (first contribution)
- Zachary Sailer (first contribution)
- Zaid Ur-Rehman (first contribution)


10 July 2017: Biopython 1.70
============================

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now
dropped support for Python 3.3). It has also been tested on PyPy v5.7,
PyPy3.5 v5.8 beta, and Jython 2.7 (although support for Jython is deprecated).

Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our
original logo and the current Python logo, this shows a yellow and blue snake
forming a double helix.

For installation Biopython now assumes ``setuptools`` is present, and takes
advantage of this to declare we require NumPy at install time (except under
Jython). This should help ensure ``pip install biopython`` works smoothly.

Bio.AlignIO now supports Mauve's eXtended Multi-FastA (XMFA) file format
under the format name "mauve" (contributed by Eric Rasche).

Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return
text-mode handles for use under Python 3.

Two new arguments for reading and writing blast-xml files have been added
to the Bio.SearchIO functions (read/parse and write, respectively). They
are 'use_raw_hit_ids' and 'use_raw_query_ids'. Check out the relevant
SearchIO.BlastIO documentation for a complete description of what these
arguments do.

Bio.motifs was updated to support changes in MEME v4.11.4 output.

The Bio.Seq sequence objects now have a ``.count_overlap()`` method to
supplement the Python string like non-overlap based ``.count()`` method.

The Bio.SeqFeature location objects can now be compared for equality.

Bio.Phylo.draw_graphviz is now deprecated. We recommend using Bio.Phylo.draw
instead, or another library or program if more advanced plotting functionality
is needed.

In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously
_DistanceMatrix) has a new method 'format_phylip' to write Phylip-compatible
distance matrix files (contributed by Jordan Willis).

Additionally, a number of small bugs have been fixed with further additions
to the test suite, and there has been further work to follow the Python PEP8,
PEP257 and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Aaron Kitzmiller (first contribution)
- Adil Iqbal (first contribution)
- Allis Tauri
- Andrew Guy
- Ariel Aptekmann (first contribution)
- Ben Fulton
- Bertrand Caron (first contribution)
- Chris Rands (first contribution)
- Connor T. Skennerton
- Eric Rasche
- Eric Talevich
- Francesco Gastaldello
- François Coste (first contribution)
- Frederic Sapet (first contribution)
- Jimmy O'Donnell (first contribution)
- Jared Andrews (first contribution)
- John Kern (first contribution)
- Jordan Willis (first contribution)
- João Rodrigues
- Kai Blin
- Markus Piotrowski
- Mateusz Korycinski (first contribution)
- Maximilian Greil
- Michiel de Hoon
- morrme (first contribution)
- Noam Kremen (first contribution)
- Patrick Kunzmann (first contribution)
- Peter Cock
- Rasmus Fonseca (first contribution)
- Rodrigo Dorantes-Gilardi (first contribution)
- Sacha Laurent (first contribution)
- Sourav Singh
- Ted Cybulski (first contribution)
- Tiago Antao
- Wibowo 'Bow' Arindrarto
- Zheng Ruan


6 April 2017: Biopython 1.69
============================

This release of Biopython supports Python 2.7, 3.3, 3.4, 3.5 and 3.6 (we have
now dropped support for Python 2.6). It has also been tested on PyPy v5.7,
PyPy3.5 v5.7 beta, and Jython 2.7.

We have started to dual-license Biopython under both our original liberal
"Biopython License Agreement", and the very similar but more commonly used
"3-Clause BSD License". In this release a small number of the Python files
are explicitly available under either license, but most of the code remains
under the "Biopython License Agreement" only. See the ``LICENSE.rst`` file
for more details.

We now expect and take advantage of NumPy under PyPy, and compile most of the
Biopython C code modules as well.

Bio.AlignIO now supports the UCSC Multiple Alignment Format (MAF) under the
format name "maf", using new module Bio.AlignIO.MafIO which also offers
indexed access to these potentially large files using SQLite3 (contributed by
Andrew Sczesnak, with additional refinements from Adam Novak).

Bio.SearchIO.AbiIO has been extended to support parsing FSA files. The
underlying format (ABIF) remains the same as AB1 files and so the string
'abif' is the expected format argument in the main SeqIO functions. AbiIO
determines whether the file is AB1 or FSA based on the presence of specific
tags.

The Uniprot parser is now able to parse "submittedName" elements in XML files.

The NEXUS parser handling of internal node comments has been improved, which
should help if working with tools like the BEAST TreeAnnotator. Slashes are
now also allowed in identifiers.

New parser for ExPASy Cellosaurus, a cell line database, cell line catalogue,
and cell line ontology (contributed by Steve Marshall).

For consistency the Bio.Seq module now offers a complement function (already
available as a method on the Seq and MutableSeq objects).

The SeqFeature object's qualifiers is now an explicitly ordered dictionary
(note that as of Python 3.6 the Python dict is ordered by default anyway).
This helps reproduce GenBank/EMBL files on input/output.

The Bio.SeqIO UniProt-XML parser was updated to cope with features with
unknown locations which can be found in mass spec data.

The Bio.SeqIO GenBank, EMBL, and IMGT parsers now record the molecule type
from the LOCUS/ID line explicitly in the record.annotations dictionary.
The Bio.SeqIO EMBL parser was updated to cope with more variants seen in
patent data files, and the related IMGT parser was updated to cope with
IPD-IMGT/HLA database files after release v3.16.0 when their ID line changed.
The GenBank output now uses colon space to match current NCBI DBLINK lines.

The Bio.Affy package supports Affymetrix version 4 of the CEL file format,
in addition to version 3.

The restriction enzyme list in ``Bio.Restriction`` has been updated to the
February 2017 release of REBASE.

Bio.PDB.PDBList now can download PDBx/mmCif (new default), PDB (old default),
PDBML/XML and mmtf format protein structures.  This is inline with the RCSB
recommendation to use PDBx/mmCif and deprecate the PDB file format. Biopython
already has support for parsing mmCif files.

Additionally, a number of small bugs have been fixed with further additions
to the test suite, and there has been further work to follow the Python PEP8,
PEP257 and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Aaron Rosenfeld
- Adam Kurkiewicz (first contribution)
- Adam Novak (first contribution)
- Adrian Altenhoff (first contribution)
- Allis Tauri (first contribution)
- Andrew Dalke
- Andrew Guy (first contribution)
- Andrew Sczesnak (first contribution)
- Ben Fulton
- Bernhard Thiel (first contribution)
- Bertrand Néron
- Blaise Li (first contribution)
- Brandon Carter (first contribution)
- Brandon Invergo
- Carlos Pena
- Carlos Ríos
- Chris Warth
- Emmanuel Noutahi
- Foen Peng (first contribution)
- Francesco Gastaldello (first contribution)
- Francisco Pina-Martins (first contribution)
- Hector Martinez (first contribution)
- Jacek Śmietański
- Jack Twilley (first contribution)
- Jeroen Van Goey (first contribution)
- Joshua Meyers (first contribution)
- Kurt Graff (first contribution)
- Lenna Peterson
- Leonhard Heizinger (first contribution)
- Marcin Magnus (first contribution)
- Markus Piotrowski
- Maximilian Greil (first contribution)
- Michał J. Gajda (first contribution)
- Michiel de Hoon
- Milind Luthra (first contribution)
- Oscar G. Garcia (first contribution)
- Owen Solberg
- Peter Cock
- Richard Neher (first contribution)
- Sebastian Bassi
- Sourav Singh (first contribution)
- Spencer Bliven (first contribution)
- Stefans Mezulis
- Steve Bond
- Steve Marshall (first contribution)
- Uri Laserson
- Veronika Berman (first contribution)
- Vincent Davis
- Wibowo 'Bow' Arindrarto


25 August 2016: Biopython 1.68
==============================

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but
this will be our final release to run on Python 2.6. It has also been tested
on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Bio.PDB has been extended to parse the RSSB's new binary Macromolecular
Transmission Format (MMTF, see http://mmtf.rcsb.org), in addition to the
mmCIF and PDB file formats (contributed by Anthony Bradley). This requires
an optional external dependency on the mmtf-python library.

Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski).
It is now faster, addresses some problems with local alignments, and also
now allows gap insertions after deletions, and vice versa, inspired by the
https://doi.org/10.1101/031500 preprint from Flouri et al.

The two sample graphical tools SeqGui (Sequence Graphical User Interface)
and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter
library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide
transcription, back-transcription and translation into amino acids using
Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython.
xbbtools is able to open Fasta formatted files, does simple nucleotide
operations and translations in any reading frame using one of the NCBI genetic
codes. In addition, it supports standalone Blast installations to do local
Blast searches.

New NCBI genetic code table 26 (Pachysolen tannophilus Nuclear Code) has been
added to Bio.Data (and the translation functionality), and table 11 is now
also available under the alias Archaeal.

In line with NCBI website changes, Biopython now uses HTTPS rather than HTTP
to connect to the NCBI Entrez and QBLAST API.

Additionally, a number of small bugs have been fixed with further additions
to the test suite, and there has been further work to follow the Python PEP8
and best practice standard coding style.

Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:

- Anthony Bradley (first contribution)
- Ben Fulton
- Carlos Pena
- Connor T. Skennerton
- Iddo Friedberg
- Kai Blin
- Kristian Davidsen (first contribution)
- Markus Piotrowski
- Olivier Morelle (first contribution)
- Peter Cock
- Stefans Mezulis (first contribution)
- Tiago Antao
- Travis Wrightsman
- Uwe Schmitt (first contribution)
- Xiaoyu Zhuo (first contribution)


8 June 2016: Biopython 1.67
===========================

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but
support for Python 2.6 is considered to be deprecated. It has also been
tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Comparison of SeqRecord objects until now has used the default Python object
comparison (are they the same instance in memory?). This can be surprising, but
comparing all of the attributes would be too complex. As of this release
attempting to compare SeqRecord objects should raise an exception instead. If
you want the old behaviour, use id(record1) == id(record2) instead.

New experimental module Bio.phenotype is for working with Phenotype Microarray
plates in JSON and the machine vendor's CSV format (contributed by Marco
Galardini).

Following the convention used elsewhere in Biopython, there is a new function
Bio.KEGG.read(...) for parsing KEGG files expected to contain a single record
only - the existing function Bio.KEGG.parse(...) is intended to be used to
iterate over multi-record files.

When a gap character is defined, Bio.Seq will now translate gap codons
(e.g. "---") into a single gap ("-") in the protein sequence. The gap character
is inferred from the Seq object's alphabet, but it can also be passed as an
argument to the translate method.

The new NCBI genetic code table 25, covering Candidate Division SR1 and
Gracilibacteria, has been added to Bio.Data (and the translation
functionality).

The Bio.Entrez interface will automatically use an HTTP POST rather than
HTTP GET if the URL would exceed 1000 characters. This is based on NCBI
guidelines and the fact that very long queries like complex searches can
otherwise trigger an HTTP Error 414 Request URI too long.

Foreign keys are now used when creating BioSQL databases with SQLite3 (this
was not possible until SQLite version 3.6.19). The BioSQL taxonomy code now
updates the taxon table left/right keys when updating the taxonomy.

There have been some fixes to the MMCIF structure parser which now uses
identifiers which better match results from the PDB structure parse.

The restriction enzyme list in ``Bio.Restriction`` has been updated to the
May 2016 release of REBASE.

The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second version
which only looks at the ATOM and HETATM lines and can be much faster.

The Bio.KEGG.REST will now return unicode text-based handles, except for
images which remain as binary bytes-based handles, making