Model UTRs explicitly

[jorvis]

Kyle - This is something you requested, but could you add a comment with a bit more information? Do you just need the class to be created or do you have a file already where they could be included? (I expect a GFF file where the mRNA/exon feature coordinates are outside of the range of the CDS ones.)

Keep in mind the GFF specification (scroll down to the section labeled "The Canonical Gene")
http://www.sequenceontology.org/gff3.shtml

And the SO definition:
http://www.sequenceontology.org/miso/current_release/term/SO:0000203

[ktretina]

Hi Joshua,

I'd like UTRs to be added to this file (which certainly has genes with
UTRs):

/usr/local/projects/t_parva/annotation/Muguga-FINAL/t_parva.IGS.annotation.formatted.split.newIDs.withFunctional.20140519_1.gff3

I'd also like the class to be created because I have a bunch of motifs and
I'm looking to see where they are found in the genome, including UTRs. I
imagine using the class something like this, but please let me know what
you think.

for gene in sorted(assemblies[contig].genes()):
for mRNA in gene.mRNAs():
for five_prime_UTR in mRNA.five_prime_UTRs():
#do something, like see if the UTR overlaps my motif
for three_prime_UTR in mRNA.three_prime_UTRs():
#do something else

Does that make sense? Let me know if you are looking for anything else.
Thanks,
Kyle

On Thu, Jun 5, 2014 at 5:17 PM, Joshua Orvis [email protected]
wrote:

Kyle - This is something you requested, but could you add a comment with a
bit more information? Do you just need the class to be created or do you
have a file already where they could be included? (I expect a GFF file
where the mRNA/exon feature coordinates are outside of the range of the CDS
ones.)

Keep in mind the GFF specification (scroll down to the section labeled
"The Canonical Gene")
http://www.sequenceontology.org/gff3.shtml

And the SO definition:
http://www.sequenceontology.org/miso/current_release/term/SO:0000203

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#14.

[jorvis]

The basic classes are now added, but nothing to iterate over them yet.