[Biopython] GFF.writer

[Mic]

Hi all,
Thank you it is working fine. From SNAP I have got Eterm and Einit as
sub_features together with a score than I created a top_feature gene and
got the following gff3 file:

##gff-version 3
##sequence-region X 1 4795218
X        SNAP    gene    5974    7324    .       -       .
ID=X-snap.4;Name=UR090:UniRef90_Q9FX16;Note=F12G12.10 protein n:1
Tax:Arabidopsis thaliana RepID:Q9FX16_ARATH
X        SNAP    Eterm   5974    6007    5.650   -       .
Parent=X-snap.4
X        SNAP    Einit   6161    7324    -5.800  -       .
Parent=X-snap.4

Now I just wonder whether I should add sub_features' score together (5.650
+ (-5.800 ) = -0.1499) and the result insert to the top_feature score (
-0.1499)?

Thank you in advance.

Mic


On Tue, May 7, 2013 at 12:30 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> Peter;
>
> > Would using an OrderedDict be neater? i.e. Preserve any user
> > given order or whatever there was when parsing. This would
> > allow ad-hoc conventions like the ID is first to be observed
> > (or whatever the user preferred).
>
> The current API generates the GFF from Biopython Seq and SeqFeature
> objects, so there isn't a clean way to pass through ordering like this.
> We could expose qualifiers as OrderedDicts if that's a useful change,
> but still need to pick an ordering for non-qualifier items.
>
> Practically, there is no guaranteed order to GFF3 attributes. Exposing
> an alphabetized list seems reasonable but it's probably not worth going
> too far down this path.
>
> Brad
>