Zhiliang Hu | 1 Apr 06:05 2009

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,
(Continue reading)

Jason Stajich | 1 Apr 07:18 2009

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');  }
(Continue reading)

Zhiliang Hu | 1 Apr 10:42 2009

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:
(Continue reading)

Scott Cain | 1 Apr 16:57 2009
Picon

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
(Continue reading)

Zhiliang Hu | 1 Apr 21:59 2009

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"
>
(Continue reading)

Frédéric Sapet | 2 Apr 09:54 2009
Picon

Search Tool

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

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Scott Cain | 2 Apr 15:22 2009
Picon

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.
>
> ------------------------------------------------------------------------------
> _______________________________________________
> 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

------------------------------------------------------------------------------
Scott Cain | 2 Apr 18:22 2009
Picon

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

------------------------------------------------------------------------------
Gudmundur A. Thorisson | 2 Apr 18:41 2009
Picon

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
>>
>>

------------------------------------------------------------------------------
Frédéric Sapet | 2 Apr 18:48 2009
Picon

Re: Search Tool

Hi,

"sounds cool, you implement it"
hum, it will be not possible right now, tooooo much other things to do :)

By the way, as Lincoln suggested, I've created a feature request.

Thank you

Fred


2009/4/2 Gudmundur A. Thorisson <gthorisson <at> gmail.com>
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-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>:
>> 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 <at> lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>


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