[Bioperl-l] RE: strand in Meta-data sequence-region

[Roels, Steven]

Lincoln,

The recent discussion of GFF3 parsing on the bioperl list reminded me
about a request I made for strand info in the sequence-region meta-data
line (to handle "flipped" slices).

Not urgent - just thought I'd point it out while folks are working on
the relevant modules...

Or did something come up that indicated the suggested change was a bad
idea?

Thanks,

-Steve

>>Sent: Tuesday, January 20, 2004 7:14 AM
>>To: Roels, Steven; gff-list at sanger.ac.uk
>>Subject: Re: spaces definition
>>
>>Hi Steven,
>>
>>I missed your messages due to spam filter screw up.  With respect to
>>your first question about the strand, I will be happy to add an
>>optional strand field (plus strand assumed if missing).  Does that
>>sound OK?
>
>Perfect - thanks.
>
>>
>>Lincoln
>>>-----Original Message-----
>>>From: owner-gff-list at sanger.ac.uk
[mailto:owner-gff-list at sanger.ac.uk] On
>>>Behalf Of Roels, Steven
>>>Sent: Friday, December 12, 2003 10:21 AM
>>>To: gff-list at sanger.ac.uk
>>>Subject: strand in Meta-data sequence-region
>>>
>>>
>>>Hello all,
>>>
>>>The spec that I see (http://song.sourceforge.net/gff3.shtml) lists
the
>>>following for the sequence-region meta-data tag:
>>>
>>>##sequence-region seqid start end
>>>        The sequence segment referred to by this file, in the format
>>>        "seqid start end".  This element is optional, but strongly
>>>        encouraged because it allows parsers to perform bounds
>>>        checking on features. There may be multiple ##sequence-region
>>>        directives, each corresponding to one of the reference
>>>        sequences referred to in the body of the file.
>>>
>>>Shouldn't "strand" be included as well? I'm often playing with
>>>gene-centered slices that have been flipped as needed so that the
gene
>>>of interest is oriented low to high. Without strand here, I can't
record
>>>sequence region accurately in the GFF file. Or is there some other
way
>>>to do it that I'm missing?
>>>
>>>Thanks,
>>>
>>>-Steve




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