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Still unable to get the histograms to work on with the allele_tower glyph

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aseladassanayake

Still unable to get the histograms to work on with the allele_tower glyph

Hello,

I have tried many things and read many posts but I am still unable to get the histograms to show on the track. When I add the ‘warn’ option to the subroutine I get this in my apache error log

Use of uninitialized value $label in lc at /usr/local/lib/perl/5.12.4/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34.

0.12 at (eval 97) line 6.

0.15 at (eval 97) line 6.

0.35 at (eval 97) line 6.

I tried changing the AuthorizedFeatureFile.pm but couldn’t solve the problem.

My track definition in the snp.conf file looks like this...

[SNPFeatures]

feature = SNP

glyph = allele_tower

label = 1

alleles = sub

{

my $snp = shift;

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

return $alleles;

}

ref_strand = sub {shift->strand}

minor_allele = sub

{

my $minor = shift;

my ($minor_allele) = $minor->attributes('minor_allele');

return $minor_allele;

}

maf = sub

{

my $snp = shift;

my ($freq) = $snp->attributes('maf');

warn $freq;

return $freq;

}

fgcolor = blue

bgcolor = red

My GFF3 file looks like this...

##gff-version3

Chr10 . contig 1 700000 . . . Name=Chr10

Chr10 . SNP 616605 616605 . . . SNP=1248696;minor_allele=G;maf=0.35;alleles=G/T

Chr10 . SNP 570873 570873 . . . SNP=2289310;minor_allele=C;maf=0.15;alleles=C/G

Chr10 . SNP 565655 565655 . . . SNP=2289311;minor_allele=T;maf=0.12;alleles=T/A

All I get now is...

Any help would be greatly appreciated.

Thank you

Regards

Asela

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Barris, Wes

Re: Still unable to get the histograms to work on with the allele_tower glyph

Asela Dassanayake wrote on 2012-01-04:

> Hello,
>
>
>
> I have tried many things and read many posts but I am still unable to
> get the histograms to show on the track. When I add the ‘warn’ option
> to the subroutine I get this in my apache error log

Hi Asela,

I have virtually the same configuration and gff3 data as you and my
allele towers display histograms. Your configuration is correct.
However, there is still a problem with your gff3 data. Uppercase
keywords in the 9th column are restricted to things like "ID" or
"Name". You are using "SNP". You need to change that to "Name="
instead of "SNP=". I don't know if that will fix the display but
that is the only problem I can see in your example. I am running
GBrowse-2.43 and Bio-Graphics-2.25.

I do not get the uninitialized value error you show below.

> Use of uninitialized value $label in lc at
> /usr/local/lib/perl/5.12.4/Bio/Graphics/Browser2/AuthorizedFeatureFile.
> pm line 34.
>
> 0.12 at (eval 97) line 6.
>
> 0.12 at (eval 97) line 6.
>
> 0.12 at (eval 97) line 6.
>
> 0.12 at (eval 97) line 6.
>
> 0.15 at (eval 97) line 6.
>
> 0.15 at (eval 97) line 6.
>
> 0.15 at (eval 97) line 6.
>
> 0.15 at (eval 97) line 6.
>
> 0.35 at (eval 97) line 6.
>
> 0.35 at (eval 97) line 6.
>
> 0.35 at (eval 97) line 6.
>
> 0.35 at (eval 97) line 6.
>
>
>
>
>
> I tried changing the AuthorizedFeatureFile.pm but couldn’t solve the
> problem.
>
>
>
> My track definition in the snp.conf file looks like this...
>
>
>
> [SNPFeatures]
>
> feature = SNP
>
> glyph = allele_tower
>
> label = 1
>
> alleles = sub
>
> {
>
> my $snp = shift;
>
> my ($alleles) = $snp->attributes('alleles');
>
> return $alleles;
>
> }
> ref_strand = sub {shift->strand}
>
> minor_allele = sub
>
> {
>
> my $minor = shift;
>
> my ($minor_allele) = $minor-
>> attributes('minor_allele');
>
> return $minor_allele;
>
> }
> maf = sub
>
> {
>
> my $snp = shift;
>
> my ($freq) = $snp->attributes('maf');
>
> warn $freq;
>
> return $freq;
>
> }
> fgcolor = blue
>
> bgcolor = red
>
>
>
>
>
> My GFF3 file looks like this...
>
>
>
> ##gff-version3
>
> Chr10 . contig 1 700000 . . . Name=Chr10
>
> Chr10 . SNP 616605 616605 . . .
> SNP=1248696;minor_allele=G;maf=0.35;alleles=G/T
>
> Chr10 . SNP 570873 570873 . . .
> SNP=2289310;minor_allele=C;maf=0.15;alleles=C/G
>
> Chr10 . SNP 565655 565655 . . .
> SNP=2289311;minor_allele=T;maf=0.12;alleles=T/A
>
>
>
> All I get now is...
>
> allele_tower_with_alleles.JPG
>
>
>
> Any help would be greatly appreciated.
>
>
>
> Thank you
>
>
>
> 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.

--
Wes Barris

This email and any files transmitted with it are confidential and intended solely for the use of the addressee. If you are not the intended addressee, then you have received this email in error and any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. Please notify us immediately of your unintended receipt by reply and then delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be held liable to any person resulting from the unintended or unauthorized use of any information contained in this email or as a result of any additions or deletions of information originally contained in this email.
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