Re: Gmod-gbrowse Digest, Vol 95, Issue 5

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Re: Gmod-gbrowse Digest, Vol 95, Issue 5

Nathan Weeks
To augment Scott's response: from a quick reading of the the
Bio::Graphics::Glyph::gene code, it looks like if one specifies a
value for "sub_part", only subfeatures of that type will be rendered
(e.g., if one specifies "sub_part = exon", then UTRs won't be
rendered). Here's the relevant code (I think) in the
Bio::Graphics::Glyph::gene module:

======================================
  my @subparts;
  if ($class->option('sub_part')) {
    @subparts = $feature->get_SeqFeatures($class->option('sub_part'));
  }
  elsif ($feature->primary_tag =~ /^mRNA/i) {
    @subparts = $feature->get_SeqFeatures(qw(CDS five_prime_UTR
three_prime_UTR UTR));
  }
  else {
    @subparts = $feature->get_SeqFeatures('exon');
  }
======================================

It would be nice if sub_part accepted a list of types.

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
Crop Genome Informatics Laboratory
Iowa State University
http://weeks.public.iastate.edu/



On Thu, Apr 17, 2014 at 4:48 PM,
<[hidden email]> wrote:

> ------------------------------
>
> Message: 7
> Date: Thu, 17 Apr 2014 10:47:22 -0700 (PDT)
> From: John Portwood <[hidden email]>
> Subject: [Gmod-gbrowse] Configuring Genes to show exons and UTRs
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> I'm having an issue trying to render exons and UTRs together. Here is a
> sample of the GFF3 I'm working with:
>
> /Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .
> Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
> Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
> Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
> Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
> Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
> Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .
> Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
> Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .
> Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
> Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
> Parent=GRMZM2G129907_T01;
> Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .
> Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
> Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0
> Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
> Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
> Parent=GRMZM2G129907_T01;
> Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .
> Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
> Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
> Parent=GRMZM2G129907_T02;
> Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0
> Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
> Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .
> Parent=GRMZM2G129907_T02;
> Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .
> Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
> Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .
> Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
> Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .
> Parent=GRMZM2G129907_T03;
> Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
> Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
> Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0
> Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
> Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
> Parent=GRMZM2G129907_T03;/
>
> Using the gene glyph produces this rendering:
> <http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png>
>
> This is close to what I want, but the inner exons aren't showing. When I use
> "sub_part=exon" in this track's stanza, the exons show but the gray UTRs
> disappear:
> <http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png>
>
> I want to render a display that looks exactly like the image above, but with
> the grayed UTR regions showing in the exons. Any help on accomplishing this
> would be greatly appreciated.
>
> Thanks,
> John
>
>
>
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Configuring-Genes-to-show-exons-and-UTRs-tp5712467.html
> Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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