O|B|F News

Biopython 1.55 released

August 31, 2010 – 6:49 pm
The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release (Biopyton 1.54) and the beta release earlier in August. A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn't notice any changes ;) In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. Additionally GenBank and EMBL parsing has been sped up, the BioSQL classes act more like Python dictionaries, and Bio.PDB should handle model numbers and a missing element column better. Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our ...

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BioRuby paper published

August 26, 2010 – 8:13 pm
After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal.  The article is open access, so please take a look. BioRuby: Bioinformatics software for the Ruby programming language Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama Bioinformatics 2010; doi: 10.1093/bioinformatics/btq475

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Biopython 1.55 beta released

August 18, 2010 – 4:52 pm
We've just released a beta of Biopython 1.55 for user testing. Since Biopython 1.54 was released three months ago, we've made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we've had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we've accidentally broken things - which is why we're doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our ...

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Biopython 1.54 released

May 20, 2010 – 3:04 pm
The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes. This is the first stable release to feature the new Bio.Phylo module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and PhyloXML formats. The module is the result of Eric Talevich's Google Summer of Code project which was supported by The National Evolutionary Synthesis Center (NESCent). Biopython now supports the reading, writing and indexing of Standard Flowgram Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains behind the widely used sff_extract tool) provided code to handle SFF files and Peter Cock has integrated that code with Bio.SeqIO. Adding SFF support to SeqIO makes it possible to convert these files ...

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BioPerl has moved to GitHub

May 14, 2010 – 12:18 am
BioPerl has migrated to git and GitHub!  We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz. If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID.  Also, add the extra email (where 'DEVNAME' is your original Subversion account ID).  This should map any previous commits from the older Subversion and CVS repository to your new GitHub account. The following are ways everyone can download the latest code. Using git Note you can replace 'bioperl-live.git' with any of the repository names (bioperl-db, bioperl-run, etc).  For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP: git clone git@github.com:bioperl/bioperl-live.git git clone https://bioperl@github.com/bioperl/bioperl-live.git The open read-only link (for everyone): git clone git://github.com/bioperl/bioperl-live.git or using the mirror site: git clone ...

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O|B|F Google Summer of Code Accepted Students

May 2, 2010 – 3:37 pm
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google.  Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance ...

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Illumina FASTQ files – Read Segment Quality Control Indicator

April 30, 2010 – 3:49 am
In another quirk to the FASTQ story, recent Illumina FASTQ files don't actually use the full range of PHRED scores - and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as 'B'). Hats off to Dr Torsten Seemann for raising awareness of this issue in his post on the seqanswers.com forum, referring to a presentation by Tobias Mann of Illumina which says: The Read Segment Quality Control Indicator: At the ends of some reads, quality scores are unreliable. Illumina has an algorithm for identifying these unreliable runs of quality scores, and we use a special indicator to flag these portions of reads A quality score of 2, encoded as a "B", is used as a special indicator. A quality score of 2 does not imply a specific error rate, but rather implies that the marked region of the read should not be used for downstream analysis. Some ...

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Partial sequence files with Biopython

April 27, 2010 – 9:03 am
This is another blog post to highlight one of the neat tricks you'll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release). It is often useful to be able to extract a few records from a larger sequence file - for example, some sequences of interest from a full UniProt or GenBank dump. One obvious way to try to do this is to parse the file into an object representation (i.e. SeqRecord objects using Bio.SeqIO.parse(...)), filter to pick out the entries you want, and then write them back to disk (using Bio.SeqIO.write(...)). However, for complex file formats like GenBank this can be lossy (Bio.SeqIO does not support a 100% identical round trip), and Biopython don't currently support writing out the SwissProt plain text format used by UniProt. So, that approach won't work. Biopython 1.52 introduced a new indexing function, Bio.SeqIO.index(...), which allows a ...

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Reminder: BOSC Abstract Deadline April 15

April 7, 2010 – 1:46 am
Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at http://www.open-bio.org/wiki/BOSC_2010 for details.  Submissions will only be accepted electronically at http://events.open-bio.org/BOSC2010/openconf.php. Graduate students, don't forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award. We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. On behalf of the BOSC 2010 organizing committee, I hope to see you there!

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Making Biopython SeqIO and AlignIO easier

April 5, 2010 – 12:37 pm
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also accept filenames. This is a case of practicality beats purity (to quote the Zen of Python), and is particularly handy when doing very short scripts or working at the Python prompt. For example, filtering a FASTA file to take only entries with a minimum length of 100 can be done like this (with handles): from Bio import SeqIO in_handle = open("example.fasta", "rU") out_handle = open("long.fasta", "w") records = (rec for rec in SeqIO.parse(in_handle, "fasta") if len(rec)>100) SeqIO.write(records, out_handle, "fasta") in_handle.close() out_handle.close() Using filenames it becomes much more concise - just three lines: from Bio import SeqIO records = (rec for rec in SeqIO.parse("example.fasta", "fasta") if len(rec)>100) SeqIO.write(records, "long.fasta", "fasta") This also means Python and Biopython beginners can postpone learning about file handles a ...

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