[Bioperl-l] Getting a Gene Object

[Ewan Birney]

On Mon, 8 Dec 2003, James Wasmuth wrote:

> Dear All,
>
> I am trying to extract the CDS sequence from EBML files.  I've got so
> far as pulling back the features from the EMBL file, but noticed that
> $feat->seq->seq give me the sequence from the start to the end of the
> feature ignoring the presence of introns.

you can use $feat->spliced_seq() to get the sequences and then potentially
translate and of course you can pick up the translated sequences as a tag
from $feat with the each_tag() command. spliced_seq() is your friend here.

>
> SeqFeature::Gene seems to provide me with what I want with
> @exons=$gene->exons.  But how do I go from the EMBL file to a
> SeqFeature::Gene::GeneStructure object?  I can't seem to see where the
> required object is returned from...
>

i am not sure if anyone has written this. Solving the general case of "set
of EMBL features" --> "Gene Structure" is surprisingly hard as (for
example) the mRNA and CDS lines can be subtly different, leading to
"interesting" semantic decisions about what to do...


Of course, a 90% decent method is probably relatively easy. Contributions
welcome ;).



> Many thanks
>
> james
>
> --
> 		"I have not failed. I've just found 10,000 ways that don't work."
> 			--- Thomas Edison
>
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