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Configuration for Allele_tower Glyph

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aseladassanayake

Configuration for Allele_tower Glyph

Hello,

I need some help with GBrowse configuration. I want to use the allele_tower glyph to represent SNPs. I have been unsuccessful in getting this glyph to work. Is there any special configuration that need to be done or added into the GBrowse.conf or the SNP.conf files?

I am reading from GFF files using the Bio::DB::SeqFeature::Store adaptor.

My GFF3 file looks like this...

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles C; Alleles T

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles C; Alleles C

Chr10 . SNP 79570873 79570873 . . . SNP 2289310; Alleles C; Alleles C

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles C; Alleles C

Chr10 . SNP 79616605 79616605 . . . SNP 1248696; Alleles ?; Alleles ?

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles T; Alleles T

Chr10 . SNP 79616605 79616605 . . . SNP 1248696; Alleles G; Alleles G

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles C; Alleles C

Chr10 . SNP 79616605 79616605 . . . SNP 1248696; Alleles G; Alleles A

Chr10 . SNP 79565655 79565655 . . . SNP 2289311; Alleles C; Alleles C

And the stanza in my snp.conf looks like this

[SNPFeatures]

feature = SNP

glyph = allele_tower

stranded = 0

bgcolor = yellow

height = 10

key = SNP Features

What am I doing wrong here?

Bit lost here.... Any help would be greatly appreciated.

Thank you very much,

Asela Dassanayake

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Ellen Schofield

Re: Configuration for Allele_tower Glyph

Hello Asela,

I hope I can help.

The allele_tower glyph requires an alleles conf attribute, which returns the alleles to display.

alleles = sub {
            my $snp = shift;
            my ($alleles) = $snp->attributes('alleles');
            return $alleles;
          }

We use an alleles attribute in our GFF that we can then use access with a callback as shown:

GFF Example...
Chr10   .       SNP     79565655        79565655        .       .       .       SNP=2289311; alleles=C/T

Stanza Example....
feature    = SNP category= Variation glyph    = allele_tower alleles = sub {             my $snp = shift;             my ($alleles) = $snp->attributes('alleles');             return $alleles;           } ref_strand = sub {shift->strand} fgcolor = orange bgcolor = darkgreen

Let me know how you get on?

Yours,
Ellen.

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On 21/12/11 04:31, Asela Dassanayake wrote:

Hello,

I need some help with GBrowse configuration. I want to use the allele_tower glyph to represent SNPs. I have been unsuccessful in getting this glyph to work. Is there any special configuration that need to be done or added into the GBrowse.conf or the SNP.conf files?

I am reading from GFF files using the Bio::DB::SeqFeature::Store adaptor.

My GFF3 file looks like this...

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles C;        Alleles T

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles C;        Alleles C

Chr10   .       SNP     79570873        79570873        .       .       .       SNP     2289310;        Alleles C;        Alleles C

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles C;        Alleles C

Chr10   .       SNP     79616605        79616605        .       .       .       SNP     1248696;        Alleles ?;       Alleles ?

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles T;        Alleles T

Chr10   .       SNP     79616605        79616605        .       .       .       SNP     1248696;        Alleles G;        Alleles G

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles C;        Alleles C

Chr10   .       SNP     79616605        79616605        .       .       .       SNP     1248696;        Alleles G;        Alleles A

Chr10   .       SNP     79565655        79565655        .       .       .       SNP     2289311;        Alleles C;       Alleles C

And the stanza in my snp.conf looks like this

[SNPFeatures]

feature      = SNP

glyph        = allele_tower

stranded     = 0

bgcolor      = yellow

height       = 10

key          = SNP Features

What am I doing wrong here?

Bit lost here.... Any help would be greatly appreciated.

Thank you very much,

Asela Dassanayake
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Barris, Wes

Re: Configuration for Allele_tower Glyph

In reply to this post by aseladassanayake

Asela Dassanayake wrote on 2011-12-20:

> Hello,
>
> I need some help with GBrowse configuration. I want to use the
> allele_tower glyph to represent SNPs. I have been unsuccessful in
> getting this glyph to work. Is there any special configuration that
> need to be done or added into the GBrowse.conf or the SNP.conf files?
>
> I am reading from GFF files using the Bio::DB::SeqFeature::Store adaptor.
>
>
>
> My GFF3 file looks like this...

This does not look like gff3 data. The last column is missing the ID tag
and it appears that you have extra columns of data.

See: http://www.sequenceontology.org/gff3.shtml

> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles C; Alleles T
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles C; Alleles C
>
> Chr10 . SNP 79570873 79570873 . .
> . SNP 2289310; Alleles C; Alleles C
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles C; Alleles C
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP 1248696; Alleles ?; Alleles ?
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles T; Alleles T
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP 1248696; Alleles G; Alleles G
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles C; Alleles C
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP 1248696; Alleles G; Alleles A
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP 2289311; Alleles C; Alleles C
>
>
>
>
>
> And the stanza in my snp.conf looks like this
>
>
>
> [SNPFeatures]
>
> feature = SNP
>
> glyph = allele_tower
>
> stranded = 0
>
> bgcolor = yellow
>
> height = 10
>
> key = SNP Features
>
>
>
> What am I doing wrong here?
>
> Bit lost here.... Any help would be greatly appreciated.
>
>
>
> Thank you very much,
>
>
> Asela Dassanayake
>
>
>
> The contents of this e-mail are confidential and may be subject to
> legal privilege.
> If you are not the intended recipient you must not use, disseminate,
> distribute or reproduce all or any part of this e-mail or attachments.
> If you have received this e-mail in error, please notify the sender
> and delete all material pertaining to this e-mail. Any opinion or
> views expressed in this e-mail are those of the individual sender and
> may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.

--
Wes Barris

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aseladassanayake

Configuration for Allele_tower Glyph

In reply to this post by aseladassanayake

Hello,

I am new to GBrowse.. and I am trying to get the allele_tower glyph to work. All the other glyphs are working except for this. I started from scratch and set up a new database....

First I added this to GBrowse.conf

[snp]

description = Nutrigenomics SNPs

path = snp.conf

Then I took the volvox.conf from the tutorial, renamed it to snp.conf and changed the following.

-dir '/var/lib/gbrowse2/databases/snp'

And I removed all the other stanzas in the track configuration section and added only this stanza

[SNPFeatures]

feature = SNP

glyph = allele_tower

alleles = sub

{

my $snp = shift;

my ($alleles) = $snp->attributes('alleles');

return $alleles;

}

ref_strand = sub {shift->strand}

fgcolor = orange

bgcolor = red

So in my /var/lib/gbrowse2/databases/snp' folder I have ONLY the snp.gff3 file with the following contents

Chr10 . contig 1 80000000 . . . Name=Chr10

Chr10 . SNP 79616605 79616605 . . . SNP=1248696; alleles=G/G

Chr10 . SNP 79570873 79570873 . . . SNP=2289310; alleles=C/C

Chr10 . SNP 79565655 79565655 . . . SNP=2289311; alleles=C/C

Chr10 . SNP 79616605 79616605 . . . SNP=1248696; alleles=G/G

Chr10 . SNP 79570873 79570873 . . . SNP=2289310; alleles=C/C

Chr10 . SNP 79565655 79565655 . . . SNP=2289311; alleles=C/C

Chr10 . SNP 79616605 79616605 . . . SNP=1248696; alleles=G/G

Chr10 . SNP 79570873 79570873 . . . SNP=2289310; alleles=C/C

Chr10 . SNP 79565655 79565655 . . . SNP=2289311; alleles=C/T

Chr10 . SNP 79616605 79616605 . . . SNP=1248696; alleles=G/G

What I get is this...

Then I changed the snp.conf to the following

[SNPFeatures]

feature = SNP

glyph = box

stranded = 0

fgcolor = orange

bgcolor = red

Then I get this...

I checked to see whether I have allele_tower.pm. I do and I can find it at

/usr/local/share/perl/5.12.4/Bio/Graphics/Glyph

What am I still doing wrong? Am I defining the Chromosome correctly by putting the line

Chr10 . contig 1 80000000 . . . Name=Chr10

At the top of the GFF3 file? Is it the correct way to define the chromosome?

What else do I need to configure.. maybe I am doing something very basic wrong as I am new to GBrowse.

Any help would be greatly appreciated...Thank you very much.

Best of Regards,

Asela

The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.

Barris, Wes

Re: Configuration for Allele_tower Glyph

Asela Dassanayake wrote on 2011-12-21:

> Hello,
>
>
>
> I am new to GBrowse.. and I am trying to get the allele_tower glyph to
> work. All the other glyphs are working except for this. I started from
> scratch and set up a new database....

[...snip...]

> So in my /var/lib/gbrowse2/databases/snp' folder I have ONLY the
> snp.gff3 file with the following contents

Your gff3 data below still does not look like it is in the correct format.
There should be only 9 columns (I can't tell whether or not you are adding
a 10th column). Here is a sample of what each row should look like:

Chr10 . SNP 79616605 79616605 . . . Name=1248696;alleles=G/G

The tabs will be removed when this gets emailed. The last column is a
semi-color separated list (with no spaces).

Also, the first line in your .gff3 file should be:
##gff-version 3

> Chr10 . contig 1 80000000 . . .
> Name=Chr10
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP=1248696; alleles=G/G
>
> Chr10 . SNP 79570873 79570873 . .
> . SNP=2289310; alleles=C/C
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP=2289311; alleles=C/C
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP=1248696; alleles=G/G
>
> Chr10 . SNP 79570873 79570873 . .
> . SNP=2289310; alleles=C/C
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP=2289311; alleles=C/C
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP=1248696; alleles=G/G
>
> Chr10 . SNP 79570873 79570873 . .
> . SNP=2289310; alleles=C/C
>
> Chr10 . SNP 79565655 79565655 . .
> . SNP=2289311; alleles=C/T
>
> Chr10 . SNP 79616605 79616605 . .
> . SNP=1248696; alleles=G/G
>
>
>
> What I get is this...
>
> allel_tower.JPG
>
>
>
> Then I changed the snp.conf to the following
>
> [SNPFeatures]
>
> feature = SNP
>
> glyph = box
>
> stranded = 0
>
> fgcolor = orange
>
> bgcolor = red
>
>
>
> Then I get this...
>
>
>
> box.JPG
>
>
>
> I checked to see whether I have allele_tower.pm. I do and I can find
> it at
>
> /usr/local/share/perl/5.12.4/Bio/Graphics/Glyph
>
>
>
> What am I still doing wrong? Am I defining the Chromosome correctly by
> putting the line
>
> Chr10 . contig 1 80000000 . . .
> Name=Chr10
>
>
>
> At the top of the GFF3 file? Is it the correct way to define the
> chromosome?
>
>
>
> What else do I need to configure.. maybe I am doing something very
> basic wrong as I am new to GBrowse.
>
>
>
> Any help would be greatly appreciated...Thank you very much.
>
>
>
> Best of Regards,
>
> Asela
>
> The contents of this e-mail are confidential and may be subject to
> legal privilege.
> If you are not the intended recipient you must not use, disseminate,
> distribute or reproduce all or any part of this e-mail or attachments.
> If you have received this e-mail in error, please notify the sender
> and delete all material pertaining to this e-mail. Any opinion or
> views expressed in this e-mail are those of the individual sender and
> may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.