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

Jason Stajich jason.stajich at duke.edu
Wed Jun 15 11:42:26 EDT 2005


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?


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

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