[Bioperl-l] new GFF2 parsing/dumping routines committed...

Ewan Birney birney@ebi.ac.uk
Mon, 20 Nov 2000 23:35:55 +0000 (GMT)

On Mon, 20 Nov 2000, Mark Wilkinson wrote:

> Hi Group!
> the last two commits from me allow the import/export of (as far as I understand) properly formatted GFF2.
> to create generic features from GFF2 you would make the call as follows:
> $Feature = new SeqFeature::Generic (-gff2_string => $string);
> The most important differences between the original -gff_string and the new -gff2_string options are as follows
> (1) the fields *must be TAB-separated* (formerly it was splitting on whitespace, but that would choke on the freetext that is now allowed)
> (2) there is no default "group" tag created.  You must specify   group=MyGroup   in the attributes field
> (3) tag/value units are semicolon separated
> (4) tags can have more than one space-separated value
> (5) free-text is allowed as a value so long as it is double-quoted.
> (6) comments are allowed but are ignored (comments are at the end of the GFF line preceeded by a # symbol)

Many thanks Mark - being strict GFF2 compliant is a "good thing" 

I am pretty sure that

   (A) at least 75% of GFF will not be strict GFF2 compliant

   (B) we'll be bitching about GFF over the next 3-4 years.

hey ho. Bioinformatics eh ?