[Bioperl-l] locus_tag of features in Bio::SeqFeature->gff_string

[Jason Stajich]

http://www.sanger.ac.uk/Software/formats/GFF/ 
GFF_Spec.shtml#attribute_field

I see the a Sequence attribute field with strings containing "."  
being escaped.  I assume that is why you see this in the current  
gff_string implementation.


I don't know if this persists in GFF3 as things are slightly  
different in terms of what needs to be escaped/protected in quotes.

I think things have really grown organically wrt GFF input/output - I  
don't know if the Bio::FeatureIO system provides a more uniform  
solution for the future?

-jason

On Jun 15, 2005, at 10:14 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> I've noticed that some locus tags are reported with "'s round them and
> some are not when gff_string is called on a feature.
>
> E.g. in NC_002755.gbk, MT2384.1 comes out as "MT2384.1", and MT4034
> comes out as MT4034.  The dot seems to be the deciding factor.
>
> Not a massive issue, by any means... :-S
>
> Mick
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/