Re: "Coding Regions" does not show on Genbank file

Scott - Thank you for the reply.

Yes I meant to display the CDS information on the track.  Here is the part 
of my configuration:

[CDS]
feature      = coding
#glyph       = transcript
glyph        = cds
bgcolor      = turquoise
fgcolor      = black
height       = 10
description  = sub { my $feature = shift;
                      return $feature->attributes('product');  }
key          = Coding Regions

Any suggested changes?  (I suppose in your example: "feature =3D coding" 
-- the "3D" is non-ascii character from your mail editor?)

Zhiliang

On Tue, 31 Mar 2009, Scott Cain wrote:

> Date: Tue, 31 Mar 2009 16:16:46 -0400
> From: Scott Cain <scott@...>
> To: Zhiliang Hu <hu@...>
> Cc: gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] "Coding Regions" does not show on Genbank file
> 
> Hi Zhiliang,

Re: "Coding Regions" does not show on Genbank file

Are you doing SeqFeature::Store or Bio::DB::GFF for the adaptor?

My transcripts are drawn with this, using Bio::DB::SeqFeature which  
has 3-level (gene -> mRNA -> {CDS,exon}) containment.

feature = gene:NCBI
glyph    = gene

For CDS:
feature = gene:NCBI
glyph    = cds

-jason
On Mar 31, 2009, at 9:05 PM, Zhiliang Hu wrote:

> Scott - Thank you for the reply.
>
> Yes I meant to display the CDS information on the track.  Here is  
> the part
> of my configuration:
>
> [CDS]
> feature      = coding
> #glyph       = transcript
> glyph        = cds
> bgcolor      = turquoise
> fgcolor      = black
> height       = 10
> description  = sub { my $feature = shift;
>                      return $feature->attributes('product');  }

Re: "Coding Regions" does not show on Genbank file

Jason - I am using the "db_adaptor = Bio::DB::GFF".

I tried "Bio::DB::SeqFeature::Store" as adaptor with your sample config 
but it complains a required table 'gb_cattle.meta' does not exist.
-- What script you used to setup the GBrowse tables?  (I used

  > load_genbank.pl --create -dsn dbi:mysql:xxx ..... )

Regards,
Zhiliang

On Tue, 31 Mar 2009, Jason Stajich wrote:

> Date: Tue, 31 Mar 2009 22:18:38 -0700
> From: Jason Stajich <jason@...>
> To: Zhiliang Hu <hu@...>
> Cc: Scott Cain <scott@...>, gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] "Coding Regions" does not show on Genbank file
> 
> Are you doing SeqFeature::Store or Bio::DB::GFF for the adaptor?
>
>
> My transcripts are drawn with this, using Bio::DB::SeqFeature which
> has 3-level (gene -> mRNA -> {CDS,exon}) containment.
>
> feature = gene:NCBI
> glyph    = gene
>
>
> For CDS:

Re: "Coding Regions" does not show on Genbank file

Hi Zhiliang,

Are you using the sample config file from the contrib directory,
08.genbank.conf?  I looked at it and it had some oddities (I don't
know off hand how old it is, but it is very old).  Here are my
suggestions:

  * fix the aggregators line: it had "coding{CDS}", where it should be
just "coding"

  * Remove bgcolor and fgcolor from the track config

I also made a few changes unrelated to the cds problem: I removed the
"mRNA{exon/mRNA}" and replaced it with "processed_transcript" and
modified the mRNA track to use the processed_transcript feature and
glyph.

And yes, the "3D" is a hex ascii code for the equals sign.  I have no
idea why it appeared in your mail 

Scott

On Wed, Apr 1, 2009 at 12:05 AM, Zhiliang Hu <hu@...> wrote:
> Scott - Thank you for the reply.
>
> Yes I meant to display the CDS information on the track.  Here is the part
> of my configuration:
>
> [CDS]
> feature      = coding

Re: "Coding Regions" does not show on Genbank file

Thanks Scott -

I have done more tests... finally I did a fresh load and new conf., ... 
now the CDS shows up 

It must be something I added/changed in the config that upsets that track.
I will gradually add back my tracks, do more modification, and see...

Thank you for all helps.

Zhiliang

On Wed, 1 Apr 2009, Scott Cain wrote:

> Date: Wed, 1 Apr 2009 10:57:34 -0400
> From: Scott Cain <scott@...>
> To: Zhiliang Hu <hu@...>
> Cc: gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] "Coding Regions" does not show on Genbank file
> 
> Hi Zhiliang,
>
> Are you using the sample config file from the contrib directory,
> 08.genbank.conf?  I looked at it and it had some oddities (I don't
> know off hand how old it is, but it is very old).  Here are my
> suggestions:
>
>  * fix the aggregators line: it had "coding{CDS}", where it should be
> just "coding"
>

Search Tool

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Re: Problem with some searches on 1.69.025

Hi Bob,

Sorry for not getting back to you sooner.  Lincoln and I talked about
this on Monday and I was going to follow up and then got distracted.

I wonder if this is a data problem?  What data adaptor are you using?
Could you send a sample of your GFF that has the chromosome lines and
some of the lines that refer to BC019681?  Also, I imagine you already
checked, but is there anything in the error log when this happens?

Scott

On Mon, Mar 30, 2009 at 1:49 PM, Bob Sinclair
<bobs@...> wrote:
> I've found a problem with the way some searches are handled in 1.69.025.
> Previously, a search for a seqID returned the corresponding details
> panel if there was just one instance of that seqID in the database, but
> if a seqID occurred multiple times (when a sequence has multiple
> alignments on the assembly, or when an EnsEMBL gene ID has several
> transcript IDs) a page would be returned with a series of links to allow
> selection of the one you want.
>
> In 1.69.025 that selection page seems to be defective.
>
> On our public browser
> (http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_current/) if
> you search for NM_011283 the details page is returned, but if you search
> for BC019681, which has a few hits, a page is returned that has the
> header section down as far as the examples links but the rest of the
> screen is blank, so something that previously displayed that "which one
> do you want" page is perhaps broken. The "done" note from firefox is
> displayed at the very bottom. The URL for this returned page is
> http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_current/#search.
>
> I repeated this using IE, as well as with Safari on the mac, and the
> results are the same in all places.
>
> Thanks if you can take a look,
>
> Bob.
>
> ------------------------------------------------------------------------------
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> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

Re: Search Tool

Hi Fred,

It is not possible currently, and it is unlikely to make it into the
GBrowse 1 branch of the code.  I can't really say if how much would be
involved in getting it into the GBrowse 2 code branch, but you can
submit a feature request for it:

  http://sourceforge.net/tracker/?group_id=27707&atid=391294

Thanks,
Scott

2009/4/2 Frédéric Sapet <frederic.sapet@...>:
> Hi,
>
> I've got a question from a user of GGB :
>
> Currently if you want to show a defined interval between to points you can
> take the positions of point 1 and point 2 in the search box and search (e.g.
> Chr2:10000000..11000000). Would it be possible to use Names instead of
> positions, e.g. "Marker1..Marker2" to show the interval between these two
> markers?
>
> Do you think it would be possible to address this need ?
>
> Thank you.
>
> Fred
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

Re: Search Tool

Hi.  Wasn't there something done (or planned) quite a while ago to  
enable plugins to somehow hook into the main search box? I vaguely  
recall being interesting in doing this at some point years ago, since  
at the time the built-in free-text search heuristics didn't work for a  
certain kind of search I wanted to offer.

Hm. I can't for the life of me what the outcome was from the resulting  
discussion; most likely something along the lines of Lincoln saying  
"sounds cool, you implement it" and then I never got around to doing  
it  :)

                   Mummi, Leicester

On 2 Apr 2009, at 17:22, Scott Cain wrote:

> Hi Fred,
>
> It is not possible currently, and it is unlikely to make it into the
> GBrowse 1 branch of the code.  I can't really say if how much would be
> involved in getting it into the GBrowse 2 code branch, but you can
> submit a feature request for it:
>
>  http://sourceforge.net/tracker/?group_id=27707&atid=391294
>
> Thanks,
> Scott
>
>
> 2009/4/2 Frédéric Sapet <frederic.sapet@...>:
>> Hi,
>>
>> I've got a question from a user of GGB :
>>
>> Currently if you want to show a defined interval between to points  
>> you can
>> take the positions of point 1 and point 2 in the search box and  
>> search (e.g.
>> Chr2:10000000..11000000). Would it be possible to use Names instead  
>> of
>> positions, e.g. "Marker1..Marker2" to show the interval between  
>> these two
>> markers?
>>
>> Do you think it would be possible to address this need ?
>>
>> Thank you.
>>
>> Fred
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>

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Re: Search Tool

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