[Bioperl-l] Submission proposal: ABIF module

Chris Fields cjfields at uiuc.edu
Sun Oct 22 14:55:46 UTC 2006

On Oct 22, 2006, at 9:16 AM, Nicola Vitacolonna wrote:

> On 22/ott/06, at 15:54, Chris Fields wrote:
>> On Oct 22, 2006, at 8:04 AM, Nicola Vitacolonna wrote:
>>> Hi everybody,
>>> I would like to submit to CPAN a module for reading and parsing the
>>> ABIF files (with .ab1 suffix) [...]
>>> May I call the module Bio::ABIF? Or should I follow other
>>> conventions?
>> It depends.  Does it interact with bioperl in any way?
> No. Can you suggest a suitable pattern for the name?
> Nicola

I don't think it will be a problem to name it Bio::ABIF; there is  
already a Bio::ASN1::EntrezGene, and Rutger Vos's Bio::Phylo modules  
(the latter doesn't require BioPerl either).

Saying that, if you plan on contributing more CPAN modules with  
similar functionality (such as parsing other trace files), you might  
want to consider using a namespace that isn't limiting but doesn't  
conflict with Bioperl core (like Bio::Trace or similar, then name  
your module Bio::Trace::ABIF).  You can use search.cpan.org to check  
namespaces for conflicts.

Just as an note: we have bioperl-ext, which also parses ABI and other  
trace file formats.  It's a bit old now and needs updating, but is  
supposed to be quite fast (it uses the Staden io_lib C library via  


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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