[Bioperl-l] SeqIO alters Genbank files

Hilmar Lapp hlapp at drycafe.net
Thu Aug 25 22:29:44 EDT 2011


Could this behavior perhaps be made optional, with the default being  
off?

	-hilmar

On Aug 25, 2011, at 11:35 PM, Brian Osborne wrote:

> bioperl-l,
>
> I need to run something by you before I commit code and tests. I  
> have code that takes a Genbank file as input and creates another  
> Genbank file as output. I noticed that SeqIO - specifically  
> FTHelper.pm - was taking a tag like this in the input file:
>
> /score=100.1
>
> And adding a "note" tag, so the output file contains this:
>
> /score=100.1
> /note="score=100.1"
>
> I'm assuming that the code does this because NCBI will not accept  
> score tags and values even though Bioperl, generally speaking, does  
> not say that NCBI defines the fine details of Genbank format.
>
> On the other hand I don't like the idea that SeqIO is altering the  
> content. It also turns out that if you have code that does multiple  
> round-trips you end up with text like this:
>
> /score=100.1
> /note="score=100.1"
> /note="score=100.1"
> /note="score=100.1"
> /note="score=100.1"
>
> Should I comment out the code that's doing these edits or not?
>
> Thanks again,
>
> Brian O.
>
>
>
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-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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