[Bioperl-l] [ANNOUNCE] bioperl-ext updates and bioperl-live

Chris Fields cjfields at uiuc.edu
Sun Nov 25 13:51:42 EST 2007


I have been making some significant changes to  
Bio::SeqIO::staden::read over the last few months which incorporate  
code from Bugzilla (bugs 2074 and 2329, very kindly donated from  
Chris Bailey and Joel Martin, cheers!).

Significant Changes:

* All Inline code in staden::read are now XS-based
* A new method has been added to Bio::SeqIO::staden::read for  
optionally getting trace data (i.e. for drawing graphs).

The method ode is now implemented in Bio::SeqIO::abi, with example  
code in examples/quality/svgtrace.pl.  These changes should allow  
newer versions of Staden io_lib as well (the code is tested with  
io_lib 1.9.2), though they haven't been tested extensively as I am  
having problems compiling newer io_lib versions on my MacBook.  It's  
very likely more changes will need to be made along the way; some  
issues were found with XS compilation which appear harmless but need  
to be investigated, and trace data from other formats need to be  
evaluated.  The possibility exists that many of these changes break  
backward compatibility with older bioperl releases, though tests  
passed with bioperl 1.5.2.

Any feedback re: platform issues, test results using newer io_lib  
versions, older bioperl-versions, etc would be greatly appreciated.   
I'm hoping this will stimulate more interest in getting other bioperl- 
ext modules up-to-date with bioperl-live.

chris


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