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.
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 v5.6, PyPy3.3 v5.5 alpha, 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 file for more details.
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.
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
- FGastaldello (first contribution)
- Francisco Pina-Martins (first contribution)
- Jacek Śmietański
- Jack Twilley (first contribution)
- Jeroen Van Goey (first contribution)
- Kurt Graff (first contribution)
- Lenna Peterson
- Leonhard Heizinger (first contribution)
- Markus Piotrowski
- Michiel de Hoon
- Milind Luthra (first contribution)
- Oscar G. Garcia (first contribution)
- Owen Solberg
- Peter Cock
- Richard Neher (first contribution)
- Sourav Singh (first contribution)
- Stefans Mezulis
- Steve Bond
- Steve Marshall (first contribution)
- Uri Laserson
- Vincent Davis
- Wibowo 'Bow' Arindrarto
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 http://dx.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)
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 it easier to use with the mostly text-based parsers in Biopython.
Note that the BioSQL test configuration information is now in a new file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py as before. You can make a copy of the provided example file Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish to run the BioSQL tests.
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 standard coding style, and in converting our docstring documentation to use the reStructuredText markup style.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Aaron Rosenfeld (first contribution)
- Anders Pitman (first contribution)
- Barbara Mühlemann (first contribution)
- Ben Fulton
- Ben Woodcroft (first contribution)
- Brandon Invergo
- Brian Osborne (first contribution)
- Carlos Pena
- Chaitanya Gupta (first contribution)
- Chris Warth (first contribution)
- Christiam Camacho (first contribution)
- Connor T. Skennerton
- David Koppstein (first contribution)
- Eric Talevich
- Jacek Śmietański (first contribution)
- João D Ferreira (first contribution)
- João Rodrigues
- Joe Cora (first contribution)
- Kai Blin
- Leighton Pritchard
- Lenna Peterson
- Marco Galardini (first contribution)
- Markus Piotrowski
- Matt Ruffalo (first contribution)
- Matteo Sticco (first contribution)
- Nader Morshed (first contribution)
- Owen Solberg (first contribution)
- Peter Cock
- Steve Bond (first contribution)
- Terry Jones (first contribution)
- Vincent Davis
- Zheng Ruan
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 2.4 to 2.6, PyPy3 version 2.4, and Jython 2.7.
Further work on the Bio.KEGG and Bio.Graphics modules now allows drawing KGML pathways with transparency.
The Bio.SeqIO "abi" parser now decodes almost all the documented fields used by the ABIF instruments - including the individual color channels.
Bio.PDB now has a QCPSuperimposer module using the Quaternion Characteristic Polynomial algorithm for superimposing structures. This is a fast alternative to the existing SVDSuperimposer code using singular value decomposition.
Bio.Entrez now implements the NCBI Entrez Citation Matching function (ECitMatch), which retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings.
Bio.Entrez.parse(...) now supports NCBI XML files using XSD schemas, which will be downloaded and cached like NCBI DTD files.
A subtle bug in how multi-part GenBank/EMBL locations on the reverse strand were parsed into CompoundLocations was fixed: complement(join(...)) as used by NCBI worked, but join(complement(...),complement(...),...) as used by EMBL/ENSEMBL gave the CompoundLocation parts in the wrong order. A related bug when taking the reverse complement of a SeqRecord containing features with CompoundLocations was also fixed.
Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work on conforming to the Python PEP8 standard coding style.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Alan Medlar (first contribution)
- Anthony Mathelier (first contribution)
- Antony Lee (first contribution)
- Anuj Sharma (first contribution)
- Ben Fulton (first contribution)
- Bertrand Néron
- Brandon Invergo
- Carlos Pena
- Christian Brueffer
- Connor T. Skennerton (first contribution)
- David Arenillas (first contribution)
- David Nicholson (first contribution)
- Emmanuel Noutahi (first contribution)
- Eric Rasche (first contribution)
- Fabio Madeira (first contribution)
- Franco Caramia (first contribution)
- Gert Hulselmans (first contribution)
- Gleb Kuznetsov (first contribution)
- João Rodrigues
- John Bradley (first contribution)
- Kai Blin
- Kian Ho (first contribution)
- Kozo Nishida (first contribution)
- Kuan-Yi Li (first contribution)
- Leighton Pritchard
- Lucas Sinclair
- Michiel de Hoon
- Peter Cock
- Saket Choudhary
- Sunhwan Jo (first contribution)
- Tarcisio Fedrizzi (first contribution)
- Tiago Antao
- Vincent Davis
The Biopython sequence objects now use string comparison, rather than Python's object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).
The Bio.KEGG and Bio.Graphics modules have been expanded with support for the online KEGG REST API, and parsing, representing and drawing KGML pathways.
The Pterobranchia Mitochondrial genetic code has been added to Bio.Data (and the translation functionality), which is the new NCBI genetic code table 24.
The Bio.SeqIO parser for the ABI capillary file format now exposes all the raw data in the SeqRecord's annotation as a dictionary. This allows further in-depth analysis by advanced users.
Bio.SearchIO QueryResult objects now allow Hit retrieval using its alternative IDs (any IDs listed after the first one, for example as used with the NCBI BLAST NR database).
We have also done some more work applying PEP8 coding styles to Biopython.
Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.
The new experimental module Bio.CodonAlign has been renamed Bio.codonalign (and similar lower case PEP8 style module names have been used for the sub-modules within this).
Bio.SeqIO.index_db(...) and Bio.SearchIO.index_db(...) now store any relative filenames relative to the index file, rather than (as before) relative to the current directory at the time the index was built. This makes the indexes less fragile, so that they can be used from other working directories. NOTE: This change is backward compatible (old index files work as before), however relative paths in new indexes will not work on older versions of Biopython!
Biopython also seems to work fine under PyPy3 2.4 which implements Python 3.2 plus unicode string literals.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Alan Du (first contribution)
- Carlos Pena (first contribution)
- Colin Lappala (first contribution)
- Christian Brueffer
- David Bulger (first contribution)
- Eric Talevich
- Evan Parker (first contribution)
- Hongbo Zhu
- Kai Blin
- Kevin Wu (first contribution)
- Leighton Pritchard
- Leszek Pryszcz (first contribution)
- Markus Piotrowski
- Matt Shirley (first contribution)
- Mike Cariaso (first contribution)
- Peter Cock
- Seth Sims (first contribution)
- Tiago Antao
- Travis Wrightsman (first contribution)
- Tyghe Vallard (first contribution)
- Vincent Davis
- Wibowo 'Bow' Arindrarto
- Zheng Ruan
This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2.
The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan.
Bio.Phylo now has tree construction and consensus modules, from the GSoC work by Yanbo Ye.
Bio.Entrez will now automatically download and cache new NCBI DTD files for
XML parsing under the user's home directory (using ~/.biopython on
Unix like systems, and $APPDATA/biopython on Windows).
Bio.Sequencing.Applications now includes a wrapper for the samtools command line tool.
Bio.PopGen.SimCoal now also supports fastsimcoal.
SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output from hmmer3.1b1.
The 'accession' of QueryResult and Hit objects created when using the 'hmmer3-tab' format are now properly named as 'accession' (previously they were acc, deviating from the documentation).
The homology key in the aln_annotation attribute of an HSP object in Bio.SearchIO has been renamed to similarity.
The Bio.SeqUtils masses and molecular_weight function have been updated.
BioSQL can now use the mysql-connector package (available for Python 2, 3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to a MySQL database.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
- Chunlei Wu (first contribution)
- Edward Liaw (first contribution)
- Eric Talevich
- Leighton Pritchard
- Manlio Calvi (first contribution)
- Markus Piotrowski (first contribution)
- Melissa Gymrek (first contribution)
- Michiel de Hoon
- Nigel Delaney
- Peter Cock
- Saket Choudhary
- Tiago Antao
- Vincent Davis (first contribution)
- Wibowo 'Bow' Arindrarto
- Yanbo Ye (first contribution)
- Zheng Ruan (first contribution)
This release supports Python 3.3 onwards without conversion via the 2to3 library. See the Biopython 1.63 beta release notes below for details. Since the beta release we have made some minor bug fixes and test improvements.
The restriction enzyme list in Bio.Restriction has been updated to the December 2013 release of REBASE.
Additional contributors since the beta:
- Gokcen Eraslan (first contribution)
This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5).
This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.
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
Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators' .next() method. This language feature is also available under Python 2.6 and 2.7.
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)
- Konstantin Tretyakov (first contribution)
- Lenna Peterson
- Martin Mokrejs
- Nigel Delaney (first contribution)
- Peter Cock
- Sergei Lebedev (first contribution)
- Tiago Antao
- Wayne Decatur (first contribution)
- Wibowo 'Bow' Arindrarto
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)
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)
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.
A faster low level string FASTA based parser SimpleFastaParser has been added to Bio.SeqIO.FastaIO which like its sister function for FASTQ files does not have the overhead of constructing SeqRecord objects.
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
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
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
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)
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)
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)
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 Ríos (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
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 Ríos (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
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.
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)
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
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.
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.
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.
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
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.
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
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.
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.
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).
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).
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.
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.
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.
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.
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
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 generate 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.
- 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.
- 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
- 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
- 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 coersion 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
- Martel added back into the released package
- new AlignACE module by Bartek Wilczynski
- Andreas Kuntzagk fix for GenBank Iterator on empty files
- 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
- 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
- minor bug fix in NCBIStandalone.blastall
- optimization in dynamic programming code
- new modules for logistic regression and maximum entropy
- minor bug fix in ParserSupport
- minor bug fixes in SCOP package
- minor updates in the kMeans cluster selection code
- minor bug fixes in SubsMat code
- support for XML-formatted MEDLINE files
- added MultiProc.run to simplify splitting code across processors
- listfns.items now supports lists with unhashable items
- new data type for pathways
- new support for intelligenetics format
- new support for metatool format
- new support for NBRF format
- new support for generalized launching of applications
- new support for genetic algorithms
- minor bug fixes in GenBank parsing
- new support for Primer in the Emboss package
- new support for chromosome graphics
- new support for HMMs
- new support for NeuralNetwork
- slew of Martel fixes (see Martel docs)
- added package to support KEGG
- added sequtils module for computations on sequences
- added pairwise sequence alignment algorithm
- major bug fixes in UndoHandle
- format updates in PubMed
- Tk interface to kMeans clustering
- deprecated old regression testing frameworks
- deprecated Sequence.py
- Swiss-Prot parser bug fixes
- GenBank parser bug fixes
- Can now output GenBank format
- can now download many sequences at a time from GenBank
- kMeans clustering algorithm
- Kabat format now supported
- FSSP format now supported
- more functionality for alignment code
- SubsMat bug fixes and updates
- fixed memory leak in listfns bug fixes
- Martel bundled and part of the install procedure
- Medline.Parser bug fixes
- PubMed.download_many handles broken IDs better
- Refactoring of modules. X/X.py moved to X/__init__.py.
- Can search sequences for Prosite patterns at ExPASy
- Can do BLAST searches against stable URL at NCBI
- Prosite Pattern bug fixes
- GenBank parser
- Complete Seq and SeqFeatures framework
- distutils cleanup
- compile warning cleanups
- support for UniGene
- code for working with substitution matrices
- Tools.MultiProc package for rudimentary multiprocessing stuff
- Added support for multiple alignments, ClustalW
- BLAST updates, bug fixes, and BlastErrorParser
- Fixes for PSI-BLAST in master-slave mode
- Minor update in stringfns, split separators can be negated
- Added download_many function to PubMed
- xbbtools updates
- Prodoc parser now accepts a copyright at the end of a record
- Swiss-Prot parser now handles taxonomy ID tag
- Blast updates:
- bug fixes in NCBIStandalone, NCBIWWW
- some __str__ methods in Record.py implemented (incomplete)
- Tests:
- new BLAST regression tests
- prosite tests fixed
- New parsers for Rebase, Gobase
- pure python implementation of C-based tools
- Thomas Sicheritz-Ponten's xbbtools
- can now generate documentation from docstrings using HappyDoc
We had a very good Birds-of-a-Feather meeting: http://www.biopython.org/pipermail/biopython/2000-August/000360.html
- Blast updates: - now works with v2.0.14 - HSP.identities and HSP.positives now tuples - HSP.gaps added
- SCOP updates: - Lin.Iterator now works with release 50
- Starting a tutorial
- New regression tests for Prodoc
Call for Participation sent out to relevant mailing lists, news groups.
The Biopython Project (http://www.biopython.org/) is a new open collaborative effort to develop freely available Python libraries and applications that address the needs of current and future work in bioinformatics, including sequence analysis, structural biology, pathways, expression data, etc. When available, the source code will be released as open source (http://www.biopython.org/License.shtml) under terms similar to Python.
This is a Call for Participation for interested people to join the project. We are hoping to attract people from a diverse set of backgrounds to help with code development, site maintenance, scientific discussion, etc. This project is open to everyone. If you're interested, please visit the web page, join the biopython mailing list, and let us know what you think!
Jeffrey Chang <[email protected]> Andrew Dalke <[email protected]>