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 http://biopython.org/wiki/News online. The latest news is at the top. =================================================================== 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 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 epecially 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). =================================================================== June 29, 2008: Biopython 1.46 released. Bio.Entrez now has several Entrez format XML parsers, and a chapter in the tutorial. Addition of new Bio.AlignIO module for working with sequence alignments in the style introduced with Bio.SeqIO in recent releases, with a whole chapter in the tutorial. A problem parsing certain EMBL files was fixed. Several minor fixes were made to the NCBI BLAST XML parser, including support for the online version 2.2.18+ introduced in May 2008. The NCBIWWW.qblast() function now allows other programs (blastx, tblastn, tblastx) in addition to just blastn and blastp. Bio.EUtils has been updated to explicitly enforce the NCBI's rule of at most one query every 3 seconds, rather than assuming the user would obey this. Iterators in Bio.Medline, Bio.SCOP, Bio.Prosite, Bio.Prosite.Prodoc, Bio.SwissProt, and others to make them more generally usable. Phylip export added to Bio.Nexus. Improved handling of ambiguous nucleotides and stop codons in Bio.Seq.Translate (plus introduced a regression fixed in Biopython 1.47). =================================================================== March 22, 2008: Biopython 1.45 released. The Seq and MutableSeq objects act more like python strings, in particular str(object) now returns the full sequence as a plain string. The existing tostring() method is preserved for backwards compatibility. BioSQL has had some bugs fixed, and has an additional unit test which loads records into a database using Bio.SeqIO and then checks the records can be retrieved correctly. The DBSeq and DBSeqRecord classes now subclass the Seq and SeqRecord classes, which provides more functionality. The modules under Bio.WWW are being deprecated. Functionality in Bio.WWW.NCBI, Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy is now available from Bio.Entrez, Bio.SCOP, Bio.InterPro and Bio.ExPASy instead. Bio.Entrez was used to fix a nasty bug in Bio.GenBank. Tiago Antao has included more functionality in the Population Genetics module, Bio.PopGen. The Bio.Cluster module has been updated to be more consistent with other Biopython code. The tutorial has been updated, including devoting a whole chapter to Swiss-Prot, Prosite, Prodoc, and ExPASy. There is also a new chapter on Bio.Entrez. Bio.biblio was deprecated. =================================================================== October 28, 2007: Biopython 1.44 released. NOTE: This release includes some rather drastic code changes, which were necessary to get Biopython to work with the new release of mxTextTools. The (reverse)complement functions in Bio.Seq support ambiguous nucleotides. Bio.Kabat, which was previously deprecated, is now removed from Biopython. Bio.MarkupEditor was deprecated, as it does not appear to have any users. Bio.Blast.NCBI.qblast() updated with more URL options, thanks to a patch from Chang Soon Ong. Several fixes to the Blast parser. The deprecated Bio.Blast.NCBIWWW functions blast and blasturl were removed. The standalone Blast functions blastall, blastpgp now create XML output by default. Bio.SeqIO.FASTA and Bio.SeqIO.generic have been deprecated in favour of the new Bio.SeqIO module. Bio.FormatIO has been removed (a gradual deprecation was not possible). Please look at Bio.SeqIO for sequence input/output instead. Fix for a bug in Bio.Cluster, which caused kcluster() to hang on some platforms. Bio.expressions has been deprecated. Bio.SeqUtils.CheckSum created, including new methods from Sebastian Bassi, and functions crc32 and crc64 which were moved from Bio/crc.py. Bio.crc is now deprecated. Bio.lcc was updated and moved to Bio.SeqUtils.lcc. Bio.SwissProt parser updated to cope with recent file format updates. Bio.Fasta, Bio.KEGG and Bio.Geo updated to pure python parsers which don't rely on Martel. Numerous fixes in the Genbank parser. Several fixes in Bio.Nexus. Bio.MultiProc and Bio.Medline.NLMMedlineXML were deprecating, as they failed on some platforms, and seemed to have no users. Deprecated concurrent behavior in Bio.config.DBRegistry and timeouts in Bio.dbdefs.swissprot, which relies on Bio.MultiProc. Tiago Antao has started work on a Population Genetics module, Bio.PopGen Updates to the tutorial, including giving Bio.Seq and Bio.SeqIO a whole chapter each. =================================================================== March 17, 2007: Biopython 1.43 released. New Bio.SeqIO module for reading and writing biological sequence files in various formats, based on SeqRecord objects. This includes a new fasta parser which is much faster than Bio.Fasta, particularly for larger files. Easier to use, too. Various improvements in Bio.SeqRecord. Running Blast using Bio.Blast.NCBIStandalone now generates output in XML format by default. The new function Bio.Blast.NCBIXML.parse can parse multiple Blast records in XML format. Bio.Cluster no longer uses ranlib, but uses its own random number generator instead. Some modifications to make Bio.Cluster more compatible with the new NumPy (we're not quite there yet though). New Bio.UniGene parser. Numerous improvements in Bio.PDB. Bug fixes in Bio.SwissProt, BioSQL, Bio.Nexus, and other modules. Faster parsing of large GenBank files. New EMBL parser under Bio.GenBank and also integrated into (new) Bio.SeqIO Compilation of KDTree (C++ code) is optional (setup.py asks the user if it should be compiled). For the Windows installer, C++ code is now included. Nominating Bio.Kabat for removal. Believe it or not, even the documentation was updated. =================================================================== July 16, 2006: Biopython 1.42 released. Bio.GenBank: New parser by Peter, which doesn't rely on Martel. Numerous updates in Bio.Nexus and Bio.Geo. Bio.Cluster became (somewhat) object-oriented. Lots of bug fixes, and updates to the documentation. =================================================================== October 28, 2005: Biopython 1.41 released. Major changes: NEW: Bio.MEME -- thanks to Jason Hackney Added transcribe, translate, and reverse_complement functions to Bio.Seq that work both on Seq objects and plain strings. Major code optimization in cpairwise2module. CompareACE support added to AlignAce. Updates to Blast parsers in Bio.Blast, in particular use of the XML parser in NCBIXML contributed by Bertrand Frottier, and the BLAT parser by Yair Benita. Pairwise single-linkage hierarchical clustering in Bio.Cluster became much faster and memory-efficient, allowing clustering of large data sets. Bio.Emboss: Added command lines for einverted and palindrome. Bio.Nexus: Added support for StringIO objects. Numerous updates in Bio.PDB. Lots of fixes in the documentation. March 29, 2005: MEME parser added. Thanks to Jason Hackney =================================================================== Feb 18, 2005: Biopython 1.40 beta Major Changes since v1.30. For a full list of changes please see the CVS IMPORTANT: Biopython now works with Python version >= 2.3 NEW: Bio.Nexus -- thanks to Frank Kauff Bio.Nexus is a Nexus file parser. Nexus is a common format for phylogenetic trees. NEW: CAPS module -- Thanks to Jonathan Taylor NEW: Restriction enzyme package contributed by Frederic Sohm. This includes classes for manipulating enzymes, updating from Rebase, as well as documentation and Tests. CHANGED: Bio.PDB -- thanks to Thomas Hamelryck Added atom serial number. Epydoc style documentation. Added secondary structure support (through DSSP) Added Accessible Surface Area support (through DSSP) Added Residue Depth support (through MSMS) Added Half Sphere Exposure. Added Fragment classification of the protein backbone (see Kolodny et al., JMB, 2002) Corrected problem on Windows with PDBList (thanks to Matt Dimmic) Added StructureAlignment module to superimpose structures based on a FASTA sequence alignment. Various additions to Polypeptide. Various bug corrections in Vector. Lots of smaller bug corrections and additional features CHANGED: MutableSeq -- thanks to Michiel De Hoon Added the functions 'complement' and 'reverse_complement' to Bio.Seq's Seq and MutableSeq objects. Similar functions previous 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. =================================================================== May 14, 2004: Biopython 1.30 Affy package added for dealing with Affymetrix cel files -- thanks to Harry Zuzan. Added code for parsing Blast XML output -- thanks to Bertrand Frottier. Added code for parsing Compass output -- thanks to James Casbon. New melting temperature calculation module -- thanks to Sebastian Bassi. Added lowess function for non-parameteric regression -- thanks to Michiel. Reduced protein alphabet supported added -- thanks to Iddo. Added documentation for Logistic Regression and Bio.PDB -- thanks to Michiel and Thomas. Documentation added for converting between file formats. Updates to install documentation for non-root users -- thanks to Jakob Fredslund. epydoc now used for automatic generation of documentation. Fasta parser updated to use Martel for parsing and indexing, allowing better speed and dealing with large data files. Updated to Registry code. Now 'from Bio import db' gives you a number of new retrieval options, including embl, fasta, genbak, interpro, prodoc and swissprot. GenBank parser uses new Martel format. GenBank retrieval now uses EUtils instead of the old non-working entrez scripts. GenBank indexing uses standard Mindy indexing. Fix for valueless qualifiers in feature keys -- thanks to Leighton Pritchard. Numerous updated to Bio.PDB modules -- thanks to Thomas. PDB can now parse headers -- thanks to Kristian Rother. Updates to the Ace parser -- thanks to Frank Kauff and Leighton Pritchard. Added pgdb (PyGreSQL) support to BioSQL -- thanks to Marc Colosimo. Fix problems with using py2exe and Biopython -- thanks to Michael Cariaso. PSIBlast parser fixes -- thanks to Jer-Yee John Chuang and James Casbon. Fix to NCBIWWW retrieval so that HTML results are returned correctly. Fix to Clustalw to handle question marks in title names -- thanks to Ashleigh Smythe. Fix to NBRF parsing to it accepts files produced by Clustalw -- thanks to Ashleigh Smythe. Fixes to the Enyzme module -- thanks to Marc Colosimo. Fix for bugs in SeqUtils -- thanks to Frank Kauff. Fix for optional hsps in ncbiblast Martel format -- thanks to Heiko. Fix to Fasta parsing to allow # comment lines -- thanks to Karl Diedrich. Updates to the C clustering library -- thanks to Michiel. Fixes for breakage in the SCOP module and addition of regression tests to framework -- thanks to Gavin. Various fixes to Bio.Wise -- thanks to Michael. Fix for bug in FastaReader -- thanks to Micheal. Fix EUtils bug where efetch would only return 500 sequences. Updates for Emboss commandlines, water and tranalign. Fixes to the FormatIO system of file conversion. C++ code (KDTree, Affy) now compiled by default on most platforms -- thanks to Michael for some nice distutils hacks and many people for testing. Deprecated Bio.sequtils -- use Bio.SeqUtils instead. Deprecated Bio.SVM -- use libsvm instead. Deprecated Bio.kMeans and Bio.xkMeans -- use Bio.cluster instead. Deprecated RecordFile -- doesn't appear to be finished code. Feb 16, 2004: Biopython 1.24 New parsers for Phred and Ace format files -- thanks to Frank Kauff New Code for dealing with NMR data -- thanks to Bob Bussell New SeqUtils modules for codon usage, isoelectric points and other protein properties -- thanks to Yair Benita New code for dealing with Wise contributed by Michael EZ-Retrieve sequence retrieval now supported thanks to Jeff Bio.Cluster updated along with documentation by Michiel BioSQL fixed so it now works with the current SQL schema -- thanks to Yves Bastide for patches Patches to Bio/__init__ to make it compatible with py2exe -- thanks to Leighton Pritchard Added __iter__ to all Biopython Iterators to make them Python 2.2 compatible Fixes to NCBIWWW for retrieving from NCBI -- thanks to Chris Wroe Retrieval of multiple alignment objects from BLAST records -- thanks to James Casbon Fixes to GenBank format for new tags by Peter Parsing fixes in clustalw parsed -- thanks to Greg Singer and Iddo Fasta Indexes can have a specified filename -- thanks to Chunlei Wu Fix to Prosite parser -- thanks to Mike Liang Fix in GenBank parsing -- mRNAs now get strand information Oct 18, 2003: Biopython 1.23 Fixed distribution of files in Bio/Cluster Now distributing Bio/KDTree/_KDTree.swig.C minor updates in installation code added mmCIF support for PDB files Oct 9, 2003: Biopython 1.22 Added Peter Slicker's patches for speeding up modules under Python 2.3 Fixed Martel installation. Does not install Bio.Cluster without Numeric. Distribute EUtils DTDs. Yves Bastide patched NCBIStandalone.Iterator to be Python 2.0 iterator Ashleigh's string 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 Jul 28, 2003: Biopython 1.21 Martel added back into the released package new AlignACE module by Bartek Wilczynski Andreas Kuntzagk fix for GenBank Iterator on empty files Jul 27, 2003: Biopython 1.20 added Andrew Dalke's EUtils library added Michiel de Hoon's gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman's fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler's NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman's fixes to Genbank code -- now parses whole database Kayte Lindner's LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich's patch to read T_Coffee files Larry Heisler's fix for primer3 output Bio.Medline now uses proper iterator objects copen now handles SIGTERM correctly small bugfixes and updates in Thomas Hamelryck's PDB package bugfixes and updates to SeqIO.FASTA reader updates to Registry system, conforms to 2003 hackathon OBDA spec Yu Huang patch to support tblastn in wublast expression Dec 17, 2002: Biopython 1.10 Python requirement bumped up to 2.2 hierarchy reorg, many things moved upwards into Bio namespace pairwise2 replaces fastpairwise and pairwise removed deprecated Sequence.py package minor bug fix in File.SGMLStripper added Scripts/debug/debug_blast_parser.py to diagnoze 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 Dec 18, 2001: Biopython1.00a4 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) Sept 3, 2001: Biopython1.00a3 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 July 5, 2001: Biopython1.00a2 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 Mar 3, 2001: Biopython 1.00a1 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 Nov 10, 2000: Biopython 0.90d04 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 Sept 6, 2000: Biopython 0.90d03 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 Aug17-18, 2000: Bioinformatics Open Source Conference 2000 We had a very good Birds-of-a-Feather meeting: http://www.biopython.org/pipermail/biopython/2000-August/000360.html Aug 2, 2000: Biopython 0.90d02 is released. 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 July 6, 2000: Biopython 0.90d01 is released. February 8, 2000: Anonymous CVS made available. August 1999 Biopython project founded. 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 Andrew Dalke