[Bioperl-l] Failed tests for FeatureIO

Chris Fields cjfields at uiuc.edu
Mon Sep 25 20:32:15 EDT 2006


On Sep 25, 2006, at 5:15 PM, Torsten Seemann wrote:

>> PS: is there any point to using mode() here?  As Sendu points out,  
>> no other Bioperl modules use it.  Just curious...
>
> Many file formats that people use Bioperl to parse have this layout:
>
> 	HEADER
> 	LINE(S) FOR FEATURE 1
> 	LINE(S) FOR FEATURE 2
>         ....ETC
> 	END
>
> Most of the modules (eg. Bio::Tools::*) don't parse HEADER until  
> the first call of next_feature(), kind of like a pull parser.  
> Unfortunately these same modules have methods to return data from  
> the HEADER (eg. sequence_name), which return undef if you haven't  
> read the first feature yet...
>
> My approach was to detect if the file handle was open for reading  
> in _initialize(), so that I could parse the header before the first  
> invocation of next_feature(), so that those HEADER-related methods  
> would return the correct values no matter when called. It also  
> makes the next_feature() implementation cleaner. The mode()  
> detection is needed as the file/handle could actually be for  
> write_feature() instead.
>
> If this is silly, I'll gladly accept advice for alternatives :-)

No, just curious.  I hadn't seen mode() in use before.

> A related question: the header of a .ptt file has a line describing  
> how many features are to follow after the header. How does this fit  
> into the Bio::FeatureIO model? I guess I have to buffer up all the  
> write_feature() calls, detect when the FeatureIO object is  
> destroyed/out of scope, and then write the header and buffered  
> features out?
>
> Any advice appreciated,
>
> -- 
> Dr Torsten Seemann               http://www.vicbioinformatics.com
> Victorian Bioinformatics Consortium, Monash University, Australia

I wrote an ERPIN parser a year ago that has a header followed by  
data, similar to what you have above. I just ran a check on the first  
iteration for the header, then flagged subsequent runs to bypass it.   
TMTOWTDI

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





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