Introduction

As I seem to be volunteering for more and more BioPerl documentation jobs recently, I thought I’d pool my resources and recycle some of my tuits to write a list summary. Expect these to be sporadic and incomplete; my goal is to highlight important questions, changes, fixes, and proposals, not recapitulate all list traffic. I’ll try to include appropriate links to specific messages, or at least to the parent message. It’ll probably take me awhile to get good at this, so please bear with me (and do send any suggestions).

To play a bit of catch up, I’m now going to loosely summarize the entire month of January (leaving a few topics untouched that are better addressed in February). February’s summary will be ready soon, after which you’ll see more easily digestable weekly (or perhaps bi-weekly) summaries. I’ll also be posting the HTML-ized summaries on my O’Reilly weblog with active hyperlinks.

One item from December 31 of 2002 bears mentioning: Ewan Birney released stable version 1.2, with significant new functionality, and important updates to code that makes use of NCBI web services; upgrading is highly recommended, although some of the January list activity reflects small trials and tribulations with this release.

http://makeashorterlink.com/?S17521DA3

Questions

Searching the mailing list archives
This seemed like an appropriate topic to put at the top of my list. The Bioperl-l mailing list isn’t exactly as high-traffic as perl5-porters or the linux kernel mailing list, but it is a mixture of both deeply technical development issues and novice user questions. While the BioPerl tutorial and documentation are the first places one should look for answers, the second place must be the archives of the mailing list. Brain Osborne pointed out that “the Search box is hidden below the Thanks link at www.bioperl.org”.
It wasn’t mentioned, but the “htdig” link Hilmar Lapp pointed out (which is also below the search box) does not actually index the bioperl mailing list, but seems to search all other OBF-affiliated lists (biojava, biopython, etc) …
```
http://users.bioperl.org/htdig/
```
Michal Kurowski pointed out that “the quickest way of accessing old postings seems to be a group archive from the mailman pages” and that “you can even download the whole thing and use it as a local mailbox”, which happens to be very useful if you want to write list summaries. Mailman archives are at:
```
http://bioperl.org/pipermail/bioperl-l/
```
Bioperl 1.2 builds under cygwin
John Nash reports that he was able to build the 1.2 distribution under cygwin once MakeMaker issues were overcome (in his case by upgrading to perl 5.8.0). Other tips are provided:
```
http://makeashorterlink.com/?S23631DA3
http://makeashorterlink.com/?M27643DA3
```
Getting/untarring the 1.2 distribution
Some people had trouble either FTPing the 1.2 distribution, or with successfully untarring the tarball. These problems seemed to have resolved by themselves, and may have been related to router issues at the server. For the record, bioperl-1.2 can be found at:
```
http://www.bioperl.org/ftp/DIST/bioperl-1.2.tar.gz
```
man pages with bioperl-1.2
People may have noticed that the “make” process for bioperl-1.2 does not generate nor install man pages. Ewan Birney explains, “In 1.2 we had to drop the manifyfication stage of the makefile because it was triggering a line-too-long error on some OSs due to shell constraints”. If you wish to get them back, comment (or delete) out the MY::manifypods sub in Makefile.PL
```
http://makeashorterlink.com/?F10761DA3
```
Converting ABI trace to Phred format
When asked why an ABI trace file read via SeqIO::abi didn’t generate a Bio::Seq::SeqWithQuality (a sequence with associated quality values), Aaron Mackey replied, “I’m not sure why abi.pm in the bioperl distribution doesn’t set it’s sequence factory to SeqWithQuality”; I’m still not sure why. See the fix at:
```
http://makeashorterlink.com/?H2C954DA3
```
biocorba status
When asked about the status of the biocorba project, Jason Stajich replied, “We have working bindings in java,perl,python and bridges to the respective Bio* toolkits from these bindings for servers and clients based on a slightly modified BSANE IDL spec from OMG”. He qualified that statement with “none of the original developers are using it in any of their work so development and final rounds of testing have not really happened”
```
http://makeashorterlink.com/?G57A42DA3
```
DNA Smith-Waterman
Yee Man has reimplemented the classic Smith-Waterman algorithm, with algorithmic improvements as suggested by Gotoh (affine gaps) and Myers & Miller (linear space), and wondered whether it would be a good addition to the BioPerl C-coded extension library (which currently contains a protein-only Smith-Waterman implementation by Ewan Birney, pSW.pm). Some discussion about classic (and novel) dynamic programming algorithms ensued, which eventually boiled down to a desire to have the generic (but extremely fast) Smith-Waterman code (written by Webb Miller) used by Bill Pearson’s SSEARCH implementation made more widely available as a linkable C library (which BioPerl could then subsume). Interested parties should contact me. Relatedly, to answer one of our FAQ’s yet again, if you currently want to do Smith-Waterman on DNA sequences, you should use BioPerl’s bindings to the EMBOSS suite of sequence utilities.
```
http://makeashorterlink.com/?Y20B21DA3
http://makeashorterlink.com/?M12B23DA3
```
using AUTOLOAD for get/set accessors
The BioPerl code is full of explicitly coded accessor methods; often we are asked why we don’t use more code-efficient methods of autogenerating these identical functions (via AUTOLOAD or Class::MakeMethod). The discussion is long-ranging, but it boils down to wanting every accessor to have the same functionality with respect to undef values and return value behavior, as dictated by our accessor “boilerplate” (which we kindly ask everyone to use). Yes, we know we can achieve that via sophisticated Class::MakeMethod usage, but we have bigger fish to fry at the moment. There’s another, subtler issue about interfaces and implementation method introspection, but I’ll leave that to a later discussion.
```
http://makeashorterlink.com/?Z22C32DA3
```
Bio:Seq no longer a RangeI (bug in Bio::Graphics::Panel)
Much to the consternation of Lincoln Stein (and his legions of Bio::Graphics users), BioPerl 1.2 introduced a change to Bio::Seq in that it no longer complies with the Bio::RangeI interface; see Heikki Lehvaslaiho’s “This has to be cruft!” message from November:
```
http://makeashorterlink.com/?Q53C41DA3
```
Unfortunately, Bio::Graphics::Panel relied on Bio::Seq having a “start” method, so lots of existing code broke. A number of fixes were recommended, including a) using a Bio::Seq::SeqFactory to generate Bio::LocatableSeq’s (which do implement RangeI methods), b) patching your Bio::Graphics::Panel and c) upgrading BioPerl 1.2 to the live CVS development version. A BioPerl 1.2.1 is forthcoming for this, and other reasons.
```
http://makeashorterlink.com/?R17C61DA3
http://makeashorterlink.com/?S3AC21DA3
```
complement(join(e1, e2)) vs. join(complement(e1), complement(e2))
Periodically, people ask “Is it possible to have bioperl output features in Genbank format of the form “complement(join(1..50,60..100))” rather than “join(complement(1..50),complement(60..100))?” This time it degenerated a little into a discussion about whether these two representations were semantically equivalent (short answer: yes). The answer to the original question is that BioPerl parses either representation into the same structure, which can only be “dumped” in one representation (presently, the latter).
```
http://makeashorterlink.com/?H2CC16DA3
```
GenBank bond() FT operator
Recent GenBank files have begun to exhibit a new feature location operator, “bond”, to identify dicysteine bonds in proteins and mRNA splice sites in RefSeq sequences. BioPerl has no concept of this location operator (which is really more of a feature, and would be better represented as a /bond feature table entry), and so currently dies when parsing a record containing it. A brute force fix is provided, but a better answer is yet to appear:
```
http://makeashorterlink.com/?L24D12DA3
```

Changes/Additions

SearchIO now has megablast parser
Jason Stajich writes, “The oft requested megablast parser has now been implemented in SearchIO”. This should be available in the upcoming bioperl 1.2.1 bug-fix release, as well as CVS.
```
http://makeashorterlink.com/?O29D62DA3
```
bl2seq parser needs to know report type to get strand right
No matter how hard he tried, Dave Arenillas couldn’t retrieve HSP strand information from a bl2seq (BLAST two sequences against each other) report. After “a little bit of detective work”, Jason Stajich found that the Bio::Tools::BPbl2seq report object needs to be told the program type (e.g. “blastn”) since it’s not smart enough to guess it by context alone. The patch to BPbl2seq.pm is available via CVS.
```
http://makeashorterlink.com/?M2ED52DA3
```
bioperl.rpm in biolinux.org distribution
Marc Logghe reports that “A couple of friends of mine have started up www.biolinux.org [ … and] are offering a number of rpm packages for free download like e.g. emboss, sim4, phylip, ncbiblast, …”. After some discussion about what a bugbear packaging BioPerl can be (most dependencies are not critical for the entire package, only certain subparts that may or may not be useful for a given person), Hunter Matthews chimed in that he’d likely be able to make a bioperl 1.2 rpm (he had previously made a 1.0 rpm); Hunter adds “7.3 would be the most likely target platform”. Marc Logghe later reported that “the bioperl rpm’s for RedHat and Suse are on line at http://biolinux.org/bioperl.html”
```
http://makeashorterlink.com/?S16E22DA3
```
example scripts reorganization for installation as “production” code
Spurred on by an earlier conversation regarding the perl scripts scattered between examples/ and scripts/, Brian Osborne has taken up the challenge to reorganize and reshape these so that those functional scripts with adequate POD and a .PLS suffix all live in scripts/ and get installed for “production” use. Scripts should remain in examples/ if they are simply “proof-of-concept” code, or just poorly documented. Everyone liked this, and from the CVS activity, it looks like the work is progressing.
```
http://makeashorterlink.com/?R29E32DA3
```
Bio::Seq::SequenceTrace
Chad Matsalla has added a Bio::Seq::SequenceTrace object, to “mimic the information available in a scf ‘Sequence Chromatogram File”’. It slices and dices. In the process, Chad ended up rewriting his Bio::SeqIO::scf code, “because the old module was somewhat … clunky”.
```
http://makeashorterlink.com/?R3AE25DA3
```
MLAGAN/LAGAN support
Stephen Montgomery has supplied both MLAGAN and LAGAN wrappers and parsers (the Lagan Tookit is a set of alignment programs for comparative genomics).
```
http://makeashorterlink.com/?N11F24DA3
```

Fixes

SeqIO/scf.pm bug
Tony Cox “finally got around to checking in a fix for the SeqIO/scf module when it has to deal with 8-bit encoded trace data”. It’s not yet clear where this fix stands with Chad Matsalla’s rewrite of Bio/SeqIO/scf.pm
Bio::Tools::Run::WrapperBase.pm missing from 1.2
Because of some code migration between bioperl subprojects, Bio/Tools/Run/WrapperBase.pm went missing in the 1.2 release, causing a wide variety of failures. The 1.2.1 release will address this, or you can retrieve the missing file and install it manually from here:
```
http://makeashorterlink.com/?B20015EA3
```
bug fixes in Blast HSP tiling code
After finding that for certain BLAST reports the “blast” and “psiblast” SearchIO parsers gave mildly differing values for “frac_identical” and “frac_conserved”, Jason Stajich did some auditing of the HSP tiling code and found a few inconsistencies which have since been fixed. End result: frac_identical and frac_conserved should be better behaved and actually correct.
```
http://makeashorterlink.com/?V26053EA3
```

Proposals

Project ideas for the aspiring biohacker
Periodically, we’re asked “I’d like to get involved, do you have any project ideas a newbie could work on?”. Jason Stajich shot out a few choice ideas including “blastz” SearchIO parsing, which was briefly discussed. Get involved!
```
http://makeashorterlink.com/?D28022EA3
```
Bio::Perl namespace export groups
The Bio::Perl module is a top-level, “novice” interface to a few small tidbits of BioPerl functionality. Many first-time users appreciate the simplicity of the Bio::Perl interface, and so we’d like to extend it’s reach into other “meaty” areas of BioPerl functionality. Here we talk about how we might achieve this using custom export tags (a la CGI.pm and others). Another area where someone could make a dramatic impact without writing any new modules!
```
http://makeashorterlink.com/?D4A025EA3
```

Conclusion

Well, that’s it for this installment. Stay tuned for February (a much busier month!).