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News for the Biopython Project
==============================
This file contains release notes and general news about the Biopython project.
See also the DEPRECATED file which tracks the removal of obsolete modules or
functions, and online http://biopython.org/wiki/News and
http://news.open-bio.org/news/category/obf-projects/biopython/
The latest news is at the top of this file.
===================================================================
(In progress, not released yet) Biopython 1.63
Note this release does *not* support Python 2.5 (or Jython 2.5). It supports
Python 2.5, 2.6 and 3.3 only (including alternative implementations like PyPy
and Jython). This has allowed a lot of code clean-up, wider use of context
managers (with statements), and other work to improve our Python 3 support.
The Biopython Tutorial & Cookbook, and the docstring examples in the source
code, now use the Python 3 style print function in place of the Python 2
style print statement. This language feature is available under Python 2.6
and 2.7 via:
from __future__ import print_function
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Chris Mitchell (first contribution)
Christian Brueffer
Eric Talevich
Josha Inglis (first contribution)
Lenna Peterson
Martin Mokrejs
Nigel Delaney (first contribution)
Peter Cock
Sergei Lebedev (first contribution)
Wayne Decatur (first contribution)
===================================================================
28 August 2013: Biopython 1.62 released.
This is our first release to officially support Python 3, however it is
also our final release supporting Python 2.5. Specifically this release
is supported and tested on standard Python 2.5, 2.6, 2.7 and 3.3.
It was also tested under Jython 2.5, 2.7 and PyPy 1.9, 2.0.
See the Biopython 1.62 beta release notes below for most changes. Since the
beta release we have added several minor bug fixes and test improvements.
Additional contributors since the beta:
Bertrand Néron (first contribution)
Lenna Peterson
Martin Mokrejs
Matsuyuki Shirota (first contribution)
===================================================================
15 July 2013: Biopython 1.62 beta released.
This is a beta release for testing purposes, both for new features added,
and changes to location parsing, but more importantly Biopython 1.62 will
be our first release to officially support Python 3.
Specifically we intend Biopython 1.62 to support standard Python 2.5, 2.6, 2.7
and 3.3, but the release will also be tested under Jython 2.5, 2.7 and PyPy
1.9, 2.0 as well. It will be our final release supporting Python 2.5.
The translation functions will give a warning on any partial codons (and this
will probably become an error in a future release). If you know you are dealing
with partial sequences, either pad with N to extend the sequence length to a
multiple of three, or explicitly trim the sequence.
The handling of joins and related complex features in Genbank/EMBL files has
been changed with the introduction of a CompoundLocation object. Previously
a SeqFeature for something like a multi-exon CDS would have a child SeqFeature
(under the sub_features attribute) for each exon. The sub_features property
will still be populated for now, but is deprecated and will in future be
removed. Please consult the examples in the help (docstrings) and Tutorial.
Thanks to the efforts of Ben Morris, the Phylo module now supports the file
formats NeXML and CDAO. The Newick parser is also significantly faster, and can
now optionally extract bootstrap values from the Newick comment field (like
Molphy and Archaeopteryx do). Nate Sutton added a wrapper for FastTree to
Bio.Phylo.Applications.
New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats from
UniProt-GOA.
The BioSQL module is now supported in Jython. MySQL and PostgreSQL databases
can be used. The relevant JDBC driver should be available in the CLASSPATH.
Feature labels on circular GenomeDiagram figures now support the label_position
argument (start, middle or end) in addition to the current default placement,
and in a change to prior releases these labels are outside the features which
is now consistent with the linear diagrams.
The code for parsing 3D structures in mmCIF files was updated to use the
Python standard library's shlex module instead of C code using flex.
The Bio.Sequencing.Applications module now includes a BWA command line wrapper.
Bio.motifs supports JASPAR format files with multiple position-frequence
matrices.
Additionally there have been other minor bug fixes and more unit tests.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Alexander Campbell (first contribution)
Andrea Rizzi (first contribution)
Anthony Mathelier (first contribution)
Ben Morris (first contribution)
Brad Chapman
Christian Brueffer
David Arenillas (first contribution)
David Martin (first contribution)
Eric Talevich
Iddo Friedberg
Jian-Long Huang (first contribution)
Joao Rodrigues
Kai Blin
Michiel de Hoon
Nate Sutton (first contribution)
Peter Cock
Petra Kubincová (first contribution)
Phillip Garland
Saket Choudhary (first contribution)
Tiago Antao
Wibowo 'Bow' Arindrarto
Xabier Bello (first contribution)
===================================================================
5 February 2013: Biopython 1.61 released.
GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows
an octagonal shape, like the existing BOX sigil but with the corners cut off.
JAGGY shows a box with jagged edges at the start and end, intended for things
like NNNNN regions in draft genomes. Finally BIGARROW is like the existing
ARROW sigil but is drawn straddling the axis. This is useful for drawing
vertically compact figures where you do not have overlapping genes.
New module Bio.Graphics.ColorSpiral can generate colors along a spiral path
through HSV color space. This can be used to make arbitrary 'rainbow' scales,
for example to color features or cross-links on a GenomeDiagram figure.
The Bio.SeqIO module now supports reading sequences from PDB files in two
different ways. The "pdb-atom" format determines the sequence as it appears in
the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this). Alternatively, you can use the
"pdb-seqres" format to read the complete protein sequence as it is listed in
the PDB header, if available.
The Bio.SeqUtils module how has a seq1 function to turn a sequence using three
letter amino acid codes into one using the more common one letter codes. This
acts as the inverse of the existing seq3 function.
The multiple-sequence-alignment object used by Bio.AlignIO etc now supports
an annotation dictionary. Additional support for per-column annotation is
planned, with addition and splicing to work like that for the SeqRecord
per-letter annotation.
A new warning, Bio.BiopythonExperimentalWarning, has been introduced. This
marks any experimental code included in the otherwise stable release. Such
'beta' level code is ready for wider testing, but still likely to change and
should only be tried by early adopters to give feedback via the biopython-dev
mailing list. We'd expect such experimental code to reach stable status in
one or two releases time, at which point our normal policies about trying to
preserve backwards compatibility would apply. See also the README file.
This release also includes Bow's Google Summer of Code work writing a unified
parsing framework for NCBI BLAST (assorted formats including tabular and XML),
HMMER, BLAT, and other sequence searching tools. This is currently available
with the new BiopythonExperimentalWarning to indicate that this is still
somewhat experimental. We're bundling it with the main release to get more
public feedback, but with the big warning that the API is likely to change.
In fact, even the current name of Bio.SearchIO may change since unless you
are familiar with BioPerl its purpose isn't immediately clear.
The Bio.Motif module has been updated and reorganized. To allow for a clean
deprecation of the old code, the new motif code is stored in a new module
Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif.
Additionally there have been other minor bug fixes and more unit tests.
Finally, we are phasing out support for Python 2.5. We will continue support
for at least one further release (Biopython 1.62). This could be extended
given feedback from our users (or if the Jython 2.7 release is delayed, since
the current stable release Jython 2.5 implemented Python 2.5 only). Focusing
on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Brandon Invergo
Bryan Lunt (first contribution)
Christian Brueffer (first contribution)
David Cain
Eric Talevich
Grace Yeo (first contribution)
Jeffrey Chang
Jingping Li (first contribution)
Kai Blin (first contribution)
Leighton Pritchard
Lenna Peterson
Lucas Sinclair (first contribution)
Michiel de Hoon
Nick Semenkovich (first contribution)
Peter Cock
Robert Ernst (first contribution)
Tiago Antao
Wibowo 'Bow' Arindrarto
===================================================================
25 June 2012: Biopython 1.60 released.
New module Bio.bgzf supports reading and writing BGZF files (Blocked GNU
Zip Format), a variant of GZIP with efficient random access, most commonly
used as part of the BAM file format. This uses Python's zlib library
internally, and provides a simple interface like Python's gzip library.
Using this the Bio.SeqIO indexing functions now support BGZF compressed
sequence files.
The GenBank/EMBL parser will now give a warning on unrecognised feature
locations and continue parsing (leaving the feature's location as None).
Previously it would abort with an exception, which was often unhelpful.
The Bio.PDB.MMCIFParser is now compiled by default (but is still not
available under Jython, PyPy or Python 3).
The SFF parser in Bio.SeqIO now decodes Roche 454 'universal accession
number' 14 character read names, which encode the timestamp of the run,
the region the read came from, and the location of the well.
In the Phylo module, the "draw" function for plotting tree objects has become
much more flexible, with improved support for matplotlib conventions and new
parameters for specifying branch and taxon labels. Writing in the PhyloXML
format has been updated to more closely match the output of other programs. A
wrapper for the program RAxML has been added under Bio.Phylo.Applications,
alongside the existing wrapper for PhyML.
Additionally there have been other minor bug fixes and more unit tests.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Brandon Invergo
Eric Talevich
Jeff Hussmann (first contribution)
John Comeau (first contribution)
Kamil Slowikowski (first contribution)
Kevin Jacobs
Lenna Peterson (first contribution)
Matt Fenwick (first contribution)
Peter Cock
Paul T. Bathen
Wibowo Arindrarto
===================================================================
24 February 2012: Biopython 1.59 released.
Please note that this release will *not* work on Python 2.4 (while the recent
releases have worked despite us not officially supporting this).
The position objects used in Bio.SeqFeature now act almost like integers,
making dealing with fuzzy locations in EMBL/GenBank files much easier. Note as
part of this work, the arguments to create fuzzy positions OneOfPosition and
WithinPosition have changed in a non-backwards compatible way.
The SeqFeature's strand and any database reference are now properties of the
FeatureLocation object (a more logical placement), with proxy methods for
backwards compatibility. As part of this change, if you print a location
object it will now display any strand and database reference information.
The installation setup.py now supports 'install_requires' when setuptools
is installed. This avoids the manual dialog when installing Biopython via
easy_install or pip and numpy is not installed. It also allows user libraries
that require Biopython to include it in their install_requires and get
automatical installation of dependencies.
Bio.Graphics.BasicChromosome has been extended to allow simple sub-features to
be drawn on chromosome segments, suitable to show the position of genes, SNPs
or other loci. Note Bio.Graphics requires the ReportLab library.
Bio.Graphics.GenomeDiagram has been extended to allow cross-links between
tracks, and track specific start/end positions for showing regions. This can
be used to imitate the output from the Artemis Comparison Tool (ACT).
Also, a new attribute circle_core makes it easier to have an empty space in
the middle of a circular diagram (see tutorial).
Bio.Align.Applications now includes a wrapper for command line tool Clustal
Omega for protein multiple sequence alignment.
Bio.AlignIO now supports sequential PHYLIP files (as well as interlaced
PHYLIP files) as a separate format variant.
New module Bio.TogoWS offers a wrapper for the TogoWS REST API, a web service
based in Japan offering access to KEGG, DDBJ, PDBj, CBRC plus access to some
NCBI, EBI resources including PubMed, GenBank and UniProt. This is much easier
to use than the NCBI Entrez API, but should be especially useful for Biopython
users based in Asia.
Bio.Entrez function efetch has been updated to handle the NCBI's stricter
handling of multiple ID arguments in EFetch 2.0, however the NCBI have also
changed the retmode default argument so you may need to make this explicit.
e.g. retmode="text"
Additionally there have been other minor bug fixes and more unit tests.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Andreas Wilm (first contribution)
Alessio Papini (first contribution)
Brad Chapman
Brandon Invergo
Connor McCoy
Eric Talevich
João Rodrigues
Konrad Förstner (first contribution)
Michiel de Hoon
Matej Repič (first contribution)
Leighton Pritchard
Peter Cock
===================================================================
18 August 2011: Biopython 1.58 released.
A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum
Likelihood) package of programs, supporting codeml, baseml and yn00 as well
as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.
Bio.SeqIO now includes read and write support for the SeqXML, a simple XML
format offering basic annotation support. See Schmitt et al (2011) in
Briefings in Bioinformatics, http://dx.doi.org/10.1093/bib/bbr025
Bio.SeqIO now includes read support for ABI files ("Sanger" capillary
sequencing trace files, containing called sequence with PHRED qualities).
The Bio.AlignIO "fasta-m10" parser was updated to cope with the >>><<< lines
as used in Bill Pearson's FASTA version 3.36, without this fix the parser
would only return alignments for the first query sequence.
The Bio.AlignIO "phylip" parser and writer now treat a dot/period in the
sequence as an error, in line with the official PHYLIP specification. Older
versions of our code didn't do anything special with this character. Also,
support for "phylip-relaxed" has been added which allows longer record names
as used in RAxML and PHYML.
Of potential interest to anyone subclassing Biopython objects, any remaining
"old style" Python classes have been switched to "new style" classes. This
allows things like defining properties.
Bio.HMM's Viterbi algorithm now expects the initial probabilities explicitly.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Aaron Gallagher (first contribution)
Bartek Wilczynski
Bogdan T. (first contribution)
Brandon Invergo (first contribution)
Connor McCoy (first contribution)
David Cain (first contribution)
Eric Talevich
Fábio Madeira (first contribution)
Hongbo Zhu
Joao Rodrigues
Michiel de Hoon
Peter Cock
Thomas Schmitt (first contribution)
Tiago Antao
Walter Gillett
Wibowo Arindrarto (first contribution)
===================================================================
2 April 2011: Biopython 1.57 released.
Bio.SeqIO now includes an index_db() function which extends the existing
indexing functionality to allow indexing many files, and more importantly
this keeps the index on disk in a simple SQLite3 database rather than in
memory in a Python dictionary.
Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter
tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
ability to run the BLAST tools and save the output as ASN.1 format, and then
convert this to any other supported BLAST output format (plain text, tabular,
XML, or HTML) with the blast_formatter tool. The wrappers were also updated
to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.
The SeqRecord object now has a reverse_complement method (similar to that of
the Seq object). This is most useful to reversing per-letter-annotation (such
as quality scores from FASTQ) or features (such as annotation from GenBank).
Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now
uses an optimised routine for FASTQ to QUAL making this much faster.
Biopython can now be installed with pip. Thanks to David Koppstein and
James Casbon for reporting the problem.
Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and
IMGT output.
The Bio.PDB module received several fixes and improvements, including starting
to merge João's work from GSoC 2010; consequently Atom objects now know
their element type and IUPAC mass. (The new features that use these
attributes won't be included in Biopython until the next release, though, so
stay tuned.)
The nodetype hierarchy in the Bio.SCOP.Cla.Record class is now a dictionary
(previously it was a list of key,value tuples) to better match the standard.
Many thanks to the Biopython developers and community for making this release
possible, especially the following contributors:
Brad Chapman
Eric Talevich
Erick Matsen (first contribution)
Hongbo Zhu
Jeffrey Finkelstein (first contribution)
Joanna & Dominik Kasprzak (first contribution)
Joao Rodrigues
Kristian Rother
Leighton Pritchard
Michiel de Hoon
Peter Cock
Peter Thorpe (first contribution)
Phillip Garland
Walter Gillett (first contribution)
===================================================================
26 November 2010: Biopython 1.56 released.
This is planned to be our last release to support Python 2.4, however this
could be delayed given immediate feedback from our users (e.g. if this proves
to be a problem in combination with other libraries or a popular Linux
distribution).
Bio.SeqIO can now read and index UniProt XML files (under format name
"uniprot-xml", which was agreed with EMBOSS and BioPerl for when/if they
support it too).
Bio.SeqIO can now read, write and index IMGT files. These are a variant of
the EMBL sequence text file format with longer feature indentation.
Bio.SeqIO now supports protein EMBL files (used in the EMBL patents database
file epo_prt.dat) - previously we only expected nucleotide EMBL files.
The Bio.Seq translation methods and function will now accept an arbitrary
CodonTable object (for those of you working on very unusual organisms).
The SeqFeature object now supports len(feature) giving the length consistent
with the existing extract method. Also, it now supports iteration giving the
coordinate (with respect to the parent sequence) of each letter within the
feature (in frame aware order), and "in" which allows you to check if a
(parent based) coordinate is within the feature location.
Bio.Entrez will now try to download any missing NCBI DTD files and cache them
in the user's home directory.
The provisional database schema for BioSQL support on SQLite which Biopython
has been using since Release 1.53 has now been added to BioSQL, and updated
slightly.
Bio.PopGen.FDist now supports the DFDist command line tool as well as FDist2.
Bio.Motif now has a chapter in the Tutorial.
(At least) 13 people have contributed to this release, including 6 new people:
Andrea Pierleoni (first contribution)
Bart de Koning (first contribution)
Bartek Wilczynski
Bartosz Telenczuk (first contribution)
Cymon Cox
Eric Talevich
Frank Kauff
Michiel de Hoon
Peter Cock
Phillip Garland (first contribution)
Siong Kong (first contribution)
Tiago Antao
Uri Laserson (first contribution)
===================================================================
31 August 2010: Biopython 1.55 released.
See the notes below for the Biopython 1.55 beta release for changes since
Biopython 1.54 was released. Since the beta release we have marked a few
modules as obsolete or deprecated, and removed some deprecated code. There
have also been a few bug fixes, extra unit tests, and documentation
improvements.
(At least) 12 people have contributed to this release, including 6 new people:
Andres Colubri (first contribution)
Carlos Rios Vera (first contribution)
Claude Paroz (first contribution)
Cymon Cox
Eric Talevich
Frank Kauff
Joao Rodrigues (first contribution)
Konstantin Okonechnikov (first contribution)
Michiel de Hoon
Nathan Edwards (first contribution)
Peter Cock
Tiago Antao
===================================================================
18 August 2010: Biopython 1.55 beta released.
This is a beta release for testing purposes, both for new features added,
and more importantly updates to avoid code deprecated in Python 2.7 or in
Python 3. This is an important step towards Python 3 support.
We are phasing out support for Python 2.4. We will continue to support it
for at least one further release (Biopython 1.56). This could be delayed
given feedback from our users (e.g. if this proves to be a problem in
combination with other libraries or a popular Linux distribution).
The SeqRecord object now has upper and lower methods (like the Seq object and
Python strings), which return a new SeqRecord with the sequence in upper or
lower case and a copy of all the annotation unchanged.
Several small issues with Bio.PDB have been resolved, which includes better
handling of model numbers, and files missing the element column.
Feature location parsing for GenBank and EMBL files has been rewritten,
making the parser much faster.
Ace parsing by SeqIO now uses zero rather than None for the quality score of
any gaps (insertions) in the contig sequence.
The BioSQL classes DBServer and BioSeqDatabase now act more like Python
dictionaries, making it easier to count, delete, iterate over, or check for
membership of namespaces and records.
The command line tool application wrapper classes are now executable, so you
can use them to call the tool (using the subprocess module internally) and
capture the output and any error messages as strings (stdout and stderr).
This avoids having to worry about the details of how best to use subprocess.
(At least) 10 people have contributed to this release, including 5 new people:
Andres Colubri (first contribution)
Carlos Rios Vera (first contribution)
Claude Paroz (first contribution)
Eric Talevich
Frank Kauff
Joao Rodrigues (first contribution)
Konstantin Okonechnikov (first contribution)
Michiel de Hoon
Peter Cock
Tiago Antao
===================================================================
May 20, 2010: Biopython 1.54 released.
See the notes below for the Biopython 1.54 beta release for changes since
Biopython 1.53 was released. Since then there have been some changes to
the new Bio.Phylo module, more documentation, and a number of smaller
bug fixes.
===================================================================
April 2, 2010: Biopython 1.54 beta released.
We are phasing out support for Python 2.4. We will continue to support it
for at least two further releases, and at least one year (whichever takes
longer), before dropping support for Python 2.4. This could be delayed
given feedback from our users (e.g. if this proves to be a problem in
combination with other libraries or a popular Linux distribution).
New module Bio.Phylo includes support for reading, writing and working with
phylogenetic trees from Newick, Nexus and phyloXML files. This was work by
Eric Talevich on a Google Summer of Code 2009 project, under The National
Evolutionary Synthesis Center (NESCent), mentored by Brad Chapman and
Christian Zmasek.
Bio.Entrez includes some more DTD files, in particular eLink_090910.dtd,
needed for our NCBI Entrez Utilities XML parser.
The parse, read and write functions in Bio.SeqIO and Bio.AlignIO will now
accept filenames as well as handles. This follows a general shift from
other Python libraries, and does make usage a little simpler. Also
the write functions will now accept a single SeqRecord or alignment.
Bio.SeqIO now supports writing EMBL files (DNA and RNA sequences only).
The dictionary-like objects from Bio.SeqIO.index() now support a get_raw
method for most file formats, giving you the original unparsed data from the
file as a string. This is useful for selecting a subset of records from a
file where Bio.SeqIO.write() does not support the file format (e.g. the
"swiss" format) or where you need to exactly preserve the original layout.
Based on code from Jose Blanca (author of sff_extract), Bio.SeqIO now
supports reading, indexing and writing Standard Flowgram Format (SFF)
files which are used by 454 Life Sciences (Roche) sequencers. This means
you can use SeqIO to convert from SFF to FASTQ, FASTA and QUAL (as
trimmed or untrimmed reads).
An improved multiple sequence alignment object has been introduced,
and is used by Bio.AlignIO for input. This is a little stricter than the
old class but should otherwise be backwards compatible.
(At least) 11 people contributed to this release, including 5 new people:
Anne Pajon (first contribution)
Brad Chapman
Christian Zmasek
Diana Jaunzeikare (first contribution)
Eric Talevich
Jose Blanca (first contribution)
Kevin Jacobs (first contribution)
Leighton Pritchard
Michiel de Hoon
Peter Cock
Thomas Holder (first contribution)
===================================================================
December 15, 2009: Biopython 1.53 released.
Biopython is now using git for source code control, currently on github. Our
old CVS repository will remain on the OBF servers in the short/medium term
as a backup, but will not be updated in future.
The Bio.Blast.Applications wrappers now covers the new NCBI BLAST C++ tools
(where blastall is replaced by blastp, blastn, etc, and the command line
switches have all been renamed). These will be replacing the old wrappers in
Bio.Blast.NCBIStandalone which are now obsolete, and will be deprecated in
our next release.
The plain text BLAST parser has been updated, and should cope with recent
versions of NCBI BLAST, including the new C++ based version. Nevertheless,
we (and the NCBI) still recommend using the XML output for parsing.
The Seq (and related UnknownSeq) objects gained upper and lower methods,
like the string methods of the same name but alphabet aware. The Seq object
also gained a new ungap method for removing gap characters in an alphabet
aware manner.
The SeqFeature object now has an extract method, used with the parent
sequence (as a string or Seq object) to get the region of that sequence
described by the feature's location information (including the strand and
any sub-features for a join). As an example, this is useful to get the
nucleotide sequence for features in GenBank or EMBL files.
SeqRecord objects now support addition, giving a new SeqRecord with the
combined sequence, all the SeqFeatures, and any common annotation.
Bio.Entrez includes the new (Jan 2010) DTD files from the NCBI for parsing
MedLine/PubMed data.
The NCBI codon tables have been updated from version 3.4 to 3.9, which adds
a few extra start codons, and a few new tables (Tables 16, 21, 22 and 23).
Note that Table 14 which used to be called "Flatworm Mitochondrial" is now
called "Alternative Flatworm Mitochondrial", and "Flatworm Mitochondrial" is
now an alias for Table 9 ("Echinoderm Mitochondrial").
The restriction enzyme list in Bio.Restriction has been updated to the
Nov 2009 release of REBASE.
The Bio.PDB parser and output code has been updated to understand the
element column in ATOM and HETATM lines (based on patches contributed by
Hongbo Zhu and Frederik Gwinner). Bio.PDB.PDBList has also been updated
for recent changes to the PDB FTP site (Paul T. Bathen).
SQLite support was added for BioSQL databases (Brad Chapman), allowing access
to BioSQL through a lightweight embedded SQL engine. Python 2.5+ includes
support for SQLite built in, but on Python 2.4 the optional sqlite3 library
must be installed to use this. We currently use a draft BioSQL on SQLite
schema, which will be merged with the main BioSQL release for use in other
projects.
Support for running Biopython under Jython (using the Java Virtual Machine)
has been much improved thanks to input from Kyle Ellrott. Note that Jython
does not support C code - this means NumPy isn't available, and nor are a
selection of Biopython modules (including Bio.Cluster, Bio.PDB and BioSQL).
Also, currently Jython does not parse DTD files, which means the XML parser
in Bio.Entrez won't work. However, most of the Biopython modules seem fine
from testing Jython 2.5.0 and 2.5.1.
(At least) 12 people contributed to this release, including 3 first timers:
Bartek Wilczynski
Brad Chapman
Chris Lasher
Cymon Cox
Frank Kauff
Frederik Gwinner (first contribution)
Hongbo Zhu (first contribution)
Kyle Ellrott
Leighton Pritchard
Michiel de Hoon
Paul Bathen (first contribution)
Peter Cock
===================================================================
September 22, 2009: Biopython 1.52 released.
The Population Genetics module now allows the calculation of several tests,
and statistical estimators via a wrapper to GenePop. Supported are tests for
Hardy-Weinberg equilibrium, linkage disequilibrium and estimates for various
F statistics (Cockerham and Wier Fst and Fis, Robertson and Hill Fis, etc),
null allele frequencies and number of migrants among many others. Isolation
By Distance (IBD) functionality is also supported.
New helper functions Bio.SeqIO.convert() and Bio.AlignIO.convert() allow an
easier way to use Biopython for simple file format conversions. Additionally,
these new functions allow Biopython to offer important file format specific
optimisations (e.g. FASTQ to FASTA, and interconverting FASTQ variants).
New function Bio.SeqIO.index() allows indexing of most sequence file formats
(but not alignment file formats), allowing dictionary like random access to
all the entries in the file as SeqRecord objects, keyed on the record id.
This is especially useful for very large sequencing files, where all the
records cannot be held in memory at once. This supplements the more flexible
but memory demanding Bio.SeqIO.to_dict() function.
Bio.SeqIO can now write "phd" format files (used by PHRED, PHRAD and CONSED),
allowing interconversion with FASTQ files, or FASTA+QUAL files.
Bio.Emboss.Applications now includes wrappers for the "new" PHYLIP EMBASSY
package (e.g. fneighbor) which replace the "old" PHYLIP EMBASSY package (e.g.
eneighbor) whose Biopython wrappers are now obsolete.
See also the DEPRECATED file, as several old deprecated modules have finally
been removed (e.g. Bio.EUtils which had been replaced by Bio.Entrez).
On a technical note, this will be the last release using CVS for source code
control. Biopython is moving from CVS to git.
===================================================================
August 17, 2009: Biopython 1.51 released.
FASTQ support in Bio.SeqIO has been improved, extended and sped up since
Biopython 1.50. Support for Illumina 1.3+ style FASTQ files was added in the
1.51 beta release. Furthermore, we now follow the interpretation agreed on
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).
===================================================================