Incorrect source in details page

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Incorrect source in details page

by Lacey Sanderson-2 :: Rate this Message:

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I am seeing a discrepancy between the source listed in the details page and the correct one. If I hide all tracks containing Redberry sourced SNPs and then choose one (ex: L01827A) The details page still shows the source as Redberry. Notice that in the example shown below there isn't even a Redberry SNP at that position!!! I haven't done any configuration to the details page for the SNP feature and the track link = AUTO. I'm using Gbrowse 1.66

You can look at the gbrowse installation here: http://128.233.29.40/cgi-bin/gbrowse/Medicago_test/

Thanks for any help! I'm completely stumped!

Lacey

Details page for the same SNP (Names are unique to each SNP):

Name:	Lc_TOG895724_1_003_00001_Nov08_883
Type:	SNP
Source:	Redberry
Position:	chr07:24031174..24031174
Length:	1
Score:	50
Note:	"Source:UC Davis Cos
	Genotype:C
	Comment:RBvs827/P17"
load_id:	Redberry_TOG895724_chr07_24031174

>Lc_TOG895724_1_003_00001_Nov08_883 class=Sequence position=chr07:24031174..24031174
A

Note: This page uses cookies to save and restore preference information. No information is shared.
Generic genome browser version 1.66

The offending lines in the GFF:

chr07 L01827A SNP 24031174 24031174 50 . . ID=L01827A_TOG895724_chr07_24031174;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17"

chr07 P172815 SNP 24031174 24031174 50 . . ID=P172815_TOG895724_chr07_24031174;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17"

Track Stanzas:

[SNP_Eston_lensCOS]

feature = SNP:Eston

glyph = diamond

category = Lentil:Polymorphisms

description = 0

height = 10

fgcolor = white

bgcolor = sub {

my $feature = shift;

my @note = $feature->notes;

if ($note[1] =~ /.*Genotype:T.*/) {

return "crimson";

} elsif ($note[1] =~ /.*Genotype:A.*/) {

return "lawngreen";

} elsif ($note[1] =~ /.*Genotype:C.*/) {

return "blue";

} elsif ($note[1] =~ /.*Genotype:G.*/) {

return "black";

} else {

return "yellow";

}}

label = 0

link = AUTO

key = Eston SNPs

citation = SNPs generated from the UC Davis COS TOGs for the Eston line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_Redberry:lensCOS]

feature = SNP:Redberry

glyph = diamond

category = Lentil:Polymorphisms

description = 0

height = 10

fgcolor = white

bgcolor = sub {

my $feature = shift;

my @note = $feature->notes;

if ($note[1] =~ /.*Genotype:T.*/) {

return "crimson";

} elsif ($note[1] =~ /.*Genotype:A.*/) {

return "lawngreen";

} elsif ($note[1] =~ /.*Genotype:C.*/) {

return "blue";

} elsif ($note[1] =~ /.*Genotype:G.*/) {

return "black";

} else {

return "yellow";

}}

label = 0

link = AUTO

key = Redberry SNPs

citation = SNPs generated from the UC Davis COS TOGs for the Redberry line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_L01827A_lensCOS]

feature = SNP:L01827A

glyph = diamond

category = Lentil:Polymorphisms

description = 0

height = 10

fgcolor = white

bgcolor = sub {

my $feature = shift;

my @note = $feature->notes;

if ($note[1] =~ /.*Genotype:T.*/) {

return "crimson";

} elsif ($note[1] =~ /.*Genotype:A.*/) {

return "lawngreen";

} elsif ($note[1] =~ /.*Genotype:C.*/) {

return "blue";

} elsif ($note[1] =~ /.*Genotype:G.*/) {

return "black";

} else {

return "yellow";

}}

label = 0

link = AUTO

key = L01827A SNPs

citation = SNPs generated from the UC Davis COS TOGs for the L01-827A line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_P172815_lensCOS]

feature = SNP:P172815

glyph = diamond

category = Lentil:Polymorphisms

description = 0

height = 10

fgcolor = white

bgcolor = sub {

my $feature = shift;

my @note = $feature->notes;

if ($note[1] =~ /.*Genotype:T.*/) {

return "crimson";

} elsif ($note[1] =~ /.*Genotype:A.*/) {

return "lawngreen";

} elsif ($note[1] =~ /.*Genotype:C.*/) {

return "blue";

} elsif ($note[1] =~ /.*Genotype:G.*/) {

return "black";

} else {

return "yellow";

}}

label = 0

link = AUTO

key = P172815 SNPs

citation = SNPs generated from the UC Davis COS TOGs for the P172815 line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

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Re: Incorrect source in details page

by Lincoln Stein-3 :: Rate this Message:

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Do you have SNPs that share the same name? It is possible that the details page is pulling out two SNPs and only showing one (the wrong one).

Lincoln

On Fri, Oct 30, 2009 at 3:59 PM, Lacey Sanderson <las166@...> wrote:

I am seeing a discrepancy between the source listed in the details page and the correct one. If I hide all tracks containing Redberry sourced SNPs and then choose one (ex: L01827A) The details page still shows the source as Redberry. Notice that in the example shown below there isn't even a Redberry SNP at that position!!! I haven't done any configuration to the details page for the SNP feature and the track link = AUTO. I'm using Gbrowse 1.66

You can look at the gbrowse installation here: http://128.233.29.40/cgi-bin/gbrowse/Medicago_test/

Thanks for any help! I'm completely stumped!
Lacey

Details page for the same SNP (Names are unique to each SNP):
Name: Lc_TOG895724_1_003_00001_Nov08_883

Type: SNP

Source: Redberry

Position: chr07:24031174..24031174

Length: 1

Score: 50

Note: "Source:UC Davis Cos
Genotype:C
Comment:RBvs827/P17"

load_id: Redberry_TOG895724_chr07_24031174
>Lc_TOG895724_1_003_00001_Nov08_883 class=Sequence position=chr07:24031174..24031174
A
Note: This page uses cookies to save and restore preference information. No information is shared.
Generic genome browser version 1.66
The offending lines in the GFF:

chr07 L01827A SNP 24031174 24031174 50 . . ID=L01827A_TOG895724_chr07_24031174;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17"

chr07 P172815 SNP 24031174 24031174 50 . . ID=P172815_TOG895724_chr07_24031174;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17"

Track Stanzas:
[SNP_Eston_lensCOS]
feature = SNP:Eston
glyph = diamond
category = Lentil:Polymorphisms

description = 0
height = 10
fgcolor = white
bgcolor = sub {
   my $feature = shift;
   my @note = $feature->notes;

   if ($note[1] =~ /.*Genotype:T.*/) {
   return "crimson";
   } elsif ($note[1] =~ /.*Genotype:A.*/) {
   return "lawngreen";

   } elsif ($note[1] =~ /.*Genotype:C.*/) {
   return "blue";
   } elsif ($note[1] =~ /.*Genotype:G.*/) {
   return "black";

   } else {
   return "yellow";
   }}
label = 0
link = AUTO
key = Eston SNPs
citation = SNPs generated from the UC Davis COS TOGs for the Eston line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_Redberry:lensCOS]
feature = SNP:Redberry
glyph = diamond
category = Lentil:Polymorphisms
description = 0
height = 10
fgcolor = white

bgcolor = sub {
   my $feature = shift;
   my @note = $feature->notes;
   if ($note[1] =~ /.*Genotype:T.*/) {
   return "crimson";

   } elsif ($note[1] =~ /.*Genotype:A.*/) {
   return "lawngreen";
   } elsif ($note[1] =~ /.*Genotype:C.*/) {
   return "blue";

   } elsif ($note[1] =~ /.*Genotype:G.*/) {
   return "black";
   } else {
   return "yellow";

   }}
label = 0
link = AUTO
key = Redberry SNPs
citation = SNPs generated from the UC Davis COS TOGs for the Redberry line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_L01827A_lensCOS]
feature = SNP:L01827A
glyph = diamond
category = Lentil:Polymorphisms
description = 0
height = 10
fgcolor = white

bgcolor = sub {
   my $feature = shift;
   my @note = $feature->notes;
   if ($note[1] =~ /.*Genotype:T.*/) {
   return "crimson";

   } elsif ($note[1] =~ /.*Genotype:A.*/) {
   return "lawngreen";
   } elsif ($note[1] =~ /.*Genotype:C.*/) {
   return "blue";

   } elsif ($note[1] =~ /.*Genotype:G.*/) {
   return "black";
   } else {
   return "yellow";

   }}
label = 0
link = AUTO
key = L01827A SNPs
citation = SNPs generated from the UC Davis COS TOGs for the L01-827A line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.

[SNP_P172815_lensCOS]
feature = SNP:P172815
glyph = diamond
category = Lentil:Polymorphisms
description = 0
height = 10
fgcolor = white

bgcolor = sub {
   my $feature = shift;
   my @note = $feature->notes;
   if ($note[1] =~ /.*Genotype:T.*/) {
   return "crimson";

   } elsif ($note[1] =~ /.*Genotype:A.*/) {
   return "lawngreen";
   } elsif ($note[1] =~ /.*Genotype:C.*/) {
   return "blue";

   } elsif ($note[1] =~ /.*Genotype:G.*/) {
   return "black";
   } else {
   return "yellow";

   }}
label = 0
link = AUTO
key = P172815 SNPs
citation = SNPs generated from the UC Davis COS TOGs for the P172815 line. The background colours indicate the base at that location: T-red, A-green, C-blue, G-black.
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...>

------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
Gmod-gbrowse mailing list
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Re: Incorrect source in details page

by James M. Ward-2 :: Rate this Message:

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Lacey,

In case it helps, I had the same set of symptoms a couple weeks ago (during my "round robin" through all the little GBrowse2 gotchas.) It may not be your case, but for me the problem was higher up in the conf file, above the tracks. For me, it was apparently some malformed or malordered sections in the upper part of the conf file, and I resolved it by following these rules:

1) Add a specific section with the database JUST BEFORE the tracks section. (E.g. "[general:database]")
2) Reference that database for each track. (E.g. "database = general")
3) Take out almost everything above the tracks section, and one-by-one add them back. I think I had another section mixed in with the [General] section elements, and cleaning it up seemed to resolve things.

It may have been only #3 that actually fixed it.

James M. Ward
Bioinformatics and Computational Biology
Department of Neurobiology
Duke University Medical Center
james.m.ward@...
jmw86069@...
(919) 423-1107