gmod-ajax — JBrowse list

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Mitch S. <mit...@be...>]

On 07/30/2010 09:59 AM, Mitch Skinner wrote:
> UCSC does the same thing; everything is
> interbase except the numbers that it shows people.

Even though this means that the text disagrees with the graphic!  For 
example,

http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=166496530&hgt_doJsCommand=&position=chr21%3A33%2C031%2C934-33%2C031%2C938&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0

The "SOD1" gene in the image clearly starts at 33,031,934, but if you 
click on the gene then the page you get says that its coordinates are 
"chr21:33,031,935-33,041,241".

I consider this a tragedy.  And it's a source of confusion.  But it does 
seem to be an established tragedy.

Mitch

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Ian H. <ih...@be...>]

David Breimann wrote:
> That;s wired, those mess sages never reached me.

Are you subscribed to the gmod-ajax mailing list? If not, please do so - 
  it may be that you can help the next person who has questions.

Ian


>         Also, I will appreciate a response for my previous message
>         (cluases 1-5, below).
> 
> 
>     A few days ago:
>     http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
> 
>     Mitch

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

That;s wired, those mess sages never reached me.
Regarding the default view: it just that I'm working with many tracks, and
sometimes I like to "clean" things up and start from scratch. Then  simply
remove them all manually" (drag each track out of the view), but then the
list of tracks is a mess (initially, I create it ordered by some logic).
Obviously, some kind of track hierarchy or grouping (like in GBrowse) would
be even better).

And thank you for the replies.

On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner
<mit...@be...>wrote:

> On 07/30/2010 06:37 AM, David Breimann wrote:
>
>> Well, I also always use 0-based coordinates when I program (as is the rule
>> for arrays in java, perl etc.), but for the user interface - I think it's
>> better show coordinates starting from 1 (as is the rule in all biological
>> databases). For example, when looking at some gene of interest, I think the
>> user expects to see the same coordinates as will be shown in genbank, UCSC
>> genome browser etc. Otherwise, this might cause confusion.
>>
>
> I've slowly come around to thinking that we will have to support this
> unfortunate convention.  UCSC does the same thing; everything is interbase
> except the numbers that it shows people.  Hopefully we can isolate this
> weirdness to one part of the code, and not have " + 1" sprinkled all over
> the place.b
>
>
>  Also, I will appreciate a response for my previous message (cluases 1-5,
>> below).
>>
>
> A few days ago:
>
> http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
>
> Mitch
>

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Mitch S. <mit...@be...>]

On 07/30/2010 06:37 AM, David Breimann wrote:
> Well, I also always use 0-based coordinates when I program (as is the 
> rule for arrays in java, perl etc.), but for the user interface - I 
> think it's better show coordinates starting from 1 (as is the rule in 
> all biological databases). For example, when looking at some gene of 
> interest, I think the user expects to see the same coordinates as will 
> be shown in genbank, UCSC genome browser etc. Otherwise, this might 
> cause confusion.

I've slowly come around to thinking that we will have to support this 
unfortunate convention.  UCSC does the same thing; everything is 
interbase except the numbers that it shows people.  Hopefully we can 
isolate this weirdness to one part of the code, and not have " + 1" 
sprinkled all over the place.b

> Also, I will appreciate a response for my previous message (cluases 
> 1-5, below).

A few days ago:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

Mitch

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

Well, I also always use 0-based coordinates when I program (as is the rule
for arrays in java, perl etc.), but for the user interface - I think it's
better show coordinates starting from 1 (as is the rule in all biological
databases). For example, when looking at some gene of interest, I think the
user expects to see the same coordinates as will be shown in genbank, UCSC
genome browser etc. Otherwise, this might cause confusion.

Also, I will appreciate a response for my previous message (cluases 1-5,
below).

Dave


On Fri, Jul 30, 2010 at 4:27 PM, Scott Cain <sc...@sc...> wrote:

> Hi David,
>
> That's correct; JBrowse, like Chado, uses interbase coordinates, so it
> counts the spaces between bases rather than the bases themselves.
> This makes all kinds of math easier, as well as make it easier to
> unambiguously identify things like insertion and deletion points.
>
> Scott
>
>
> On Fri, Jul 30, 2010 at 9:22 AM, David Breimann
> <dav...@gm...> wrote:
> > 6. I noticed that when I click on the glyphs of feature parsed from GFF3
> > files, the start coordinate shown on the pop-up window is shifted by -1
> > relative to the actual coordinate written in the GFF file.
> >
> > On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <
> dav...@gm...>
> > wrote:
> >>
> >> Hi,
> >>
> >> 1. I would like to display some annotations from a GFF file on a single
> >> track and control their color/glyph according to the content of the note
> in
> >> the GFF (e.g. if 'Note=red' I would like this feature to be colored red,
> and
> >> if 'Note=green' I would like it to be green).
> >> 2. Can  I control for the height of the tracks (I know it can be done
> for
> >> WIG tracks, but what about normal features tracks)?
> >> 3. How can I control which tracks are shown by default?
> >> 4. Suggestion: have a "reset view" in the browser (currently I have to
> >> clear my browser history to return to the default view).
> >> 5. Is there any ETA for the improvement of the WIG tracks (most
> >> importantly adding a scale)?
> >>
> >> Keep up the good work,
> >> Dave
> >
> >
> >
> ------------------------------------------------------------------------------
> > The Palm PDK Hot Apps Program offers developers who use the
> > Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> > of $1 Million in cash or HP Products. Visit us here for more details:
> > http://p.sf.net/sfu/dev2dev-palm
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Scott C. <sc...@sc...>]

Hi David,

That's correct; JBrowse, like Chado, uses interbase coordinates, so it
counts the spaces between bases rather than the bases themselves.
This makes all kinds of math easier, as well as make it easier to
unambiguously identify things like insertion and deletion points.

Scott


On Fri, Jul 30, 2010 at 9:22 AM, David Breimann
<dav...@gm...> wrote:
> 6. I noticed that when I click on the glyphs of feature parsed from GFF3
> files, the start coordinate shown on the pop-up window is shifted by -1
> relative to the actual coordinate written in the GFF file.
>
> On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <dav...@gm...>
> wrote:
>>
>> Hi,
>>
>> 1. I would like to display some annotations from a GFF file on a single
>> track and control their color/glyph according to the content of the note in
>> the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
>> if 'Note=green' I would like it to be green).
>> 2. Can  I control for the height of the tracks (I know it can be done for
>> WIG tracks, but what about normal features tracks)?
>> 3. How can I control which tracks are shown by default?
>> 4. Suggestion: have a "reset view" in the browser (currently I have to
>> clear my browser history to return to the default view).
>> 5. Is there any ETA for the improvement of the WIG tracks (most
>> importantly adding a scale)?
>>
>> Keep up the good work,
>> Dave
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>



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

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

6. I noticed that when I click on the glyphs of feature parsed from GFF3
files, the start coordinate shown on the pop-up window is shifted by -1
relative to the actual coordinate written in the GFF file.

On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <dav...@gm...>wrote:

> Hi,
>
> 1. I would like to display some annotations from a GFF file on a single
> track and control their color/glyph according to the content of the note in
> the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
> if 'Note=green' I would like it to be green).
> 2. Can  I control for the height of the tracks (I know it can be done for
> WIG tracks, but what about normal features tracks)?
> 3. How can I control which tracks are shown by default?
> 4. Suggestion: have a "reset view" in the browser (currently I have to
> clear my browser history to return to the default view).
> 5. Is there any ETA for the improvement of the WIG tracks (most importantly
> adding a scale)?
>
> Keep up the good work,
> Dave
>

Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Ian H. <ih...@be...>]

On Jul 27, 2010, at 6:30 AM, Mitch Skinner <mit...@be...> wrote:

> 
>> 3. How can I control which tracks are shown by default?
> 
> In index.html, there's a section that looks like this:
> 
>            var b = new Browser({
>                                    containerID: "GenomeBrowser",
>                                    refSeqs: refSeqs,
>                                    trackData: trackInfo,
>                                    defaultTracks: 
> "DNA,gene,mRNA,noncodingRNA",
>                                    location: queryParams.loc,
>                                    tracks: queryParams.tracks,
>                                    bookmark: bookmarkCallback
>                                });
> 
> the "defaultTracks" setting is a comma-separated list of track labels; 
> those tracks will be shown by default.
> 
>> 4. Suggestion: have a "reset view" in the browser (currently I have to 
>> clear my browser history to return to the default view).
> 
> I don't doubt that this is useful for you, but since I don't think I've 
> heard this requested before, I'm interested in the specifics of the use 
> case.  What's the context where you want to do this?  And when you want 
> to go back to the default view, what makes the default better than what 
> you were looking at before?
> 
> For example, you might have two biological questions that you want to 
> investigate, and each of them might be addressed using a different set 
> of tracks.  So if you're looking at a bunch of tracks, and you decide 
> you want to switch all those tracks off and go look at a different set 
> of tracks, then that's one situation where I can imagine wanting to do 
> have a "reset view" option.  But I'd like to hear the specifics of your 
> case.
> 

There's also a mechanism for encoding the displayed track list in the URL, which might be relevant to points 4&5

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[Chris M. <cj...@be...>]

I created a branch of bioperl-live called "circular" and have  
committed a more circular-genome lenient version of the unflattener  
which works on NC_006578. It's quite possible that more needs to be  
done here to satisfy this part of the gff3 spec:

>> For features that cross the origin of a circular feature (e.g. most  
>> bacterial genomes, plasmids, and some viral genomes), the  
>> requirement for start to be less than or equal to end is satisfied  
>> by making end = the position of the end + the length of the  
>> landmark feature.

the current behavior generates the following for NC_006578:

NC_006578       GenBank gene    77090   77112   .       -        
1       ID=pBT9727_0001;Dbxref=GeneID:3200518;locus_tag=pBT9727_0001
NC_006578       GenBank gene    1       586     .       -        
1       ID=pBT9727_0001;Dbxref=GeneID:3200518;locus_tag=pBT9727_0001

the smart thing to do would be to translate this to a single gene  
feature:
77090.. 77698

but I'm not sure how conformant the full bio*/gmod toolchain is to  
this part of the spec

On Jul 26, 2010, at 11:14 PM, David Breimann wrote:

> Hi again guys,
>
> Here is a example:
> NC_006578.gbk from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_thuringiensis_konkukian/NC_006578.gbk 
>  has a gene that spans join(77090..77112,1..586) and it produces an  
> error:
>
> $ bp_genbank2gff3.pl -y NC_006578.gbk
> # Input: NC_006578.gbk
> # working on region:NC_006578, Bacillus thuringiensis serovar  
> konkukian str. 97-27, 23-JUL-2008, Bacillus thuringiensis serovar  
> konkukian str. 97-27 plasmid pBT9727, complete sequence.
> NC_006578 Unflattening error:
> Details:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: PROBLEM, SEVERITY==2
> Ranges not in correct order. Strange ensembl genbank entry? Range:  
> [77090,77112] [1,586]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/ 
> Root.pm:473
> STACK: Bio::SeqFeature::Tools::Unflattener::problem /usr/local/share/ 
> perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:952
> STACK:  
> Bio::SeqFeature::Tools::Unflattener::_check_order_is_consistent /usr/ 
> local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2842
> STACK: Bio::SeqFeature::Tools::Unflattener::infer_mRNA_from_CDS /usr/ 
> local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2713
> STACK: Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ 
> share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:1532
> STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:1023
> STACK: /usr/local/bin/bp_genbank2gff3.pl:506
> -----------------------------------------------------------
>
> # Possible gene unflattening error withNC_006578: consult STDERR
> # GFF3 saved to ./NC_006578.gff; DNA saved to ./NC_006578.fa
>
> Another similar example: NC_008785.gbk from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Burkholderia_mallei_SAVP1/NC_008785.gbk 
> .
>
> Best,
> Dave
>
>
> On Mon, Jul 26, 2010 at 6:20 PM, Scott Cain <sc...@sc...>  
> wrote:
> Hi Dave,
>
> Please keep your responses on the list so they can be archived.
>
> I'm also cc'ing Nathan Liles, who did the work on the genbank2gff3
> script to deal with bacterial genomes.  Perhaps Nathan can take a look
> at this genbank entry and see more quickly what the problem is.
>
> Thanks,
> Scott
>
>
>
>
> On Sun, Jul 25, 2010 at 8:26 AM, David Breimann
> <dav...@gm...> wrote:
> > Scott,
> >
> > I cloned the latest version of bioperl from github (I'm not sure  
> what you
> > mean by developers version; I thought the dev branch is obsolete  
> but I'm not
> > sure; anyway - I got the version from bioperl-live).
> > bp_genbank2gff3.pl fails exactly on features which are on the  
> margin, e.g.
> > "Ranges not in correct order. Strange ensembl genbank entry? Range:
> > [207497,208369] [1,687]".
> >
> > Thanks,
> > Dave
> >
> > On Fri, Jul 23, 2010 at 6:10 PM, Scott Cain <sc...@sc...>  
> wrote:
> >> Hi David,
> >>
> >> The NCBI GFF3 is notoriously bad and doesn't pass validation at the
> >> GFF3 validator:
> >>
> >>  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
> >>
> >> The most notable problems actually have to do with the  
> relationships
> >> between features.  For example, in the first few lines:
> >>
> >> NC_007777.1     RefSeq  gene    35      1723    .       +       .
> >>  locus_tag=Francci3_0001;db_xref=GeneID:3902947
> >> NC_007777.1     RefSeq  CDS     35      1720    .       +       0
> >>  locus_tag=Francci3_0001;transl_table=11;product=chromosomal
> >> replication initiator protein
> >>
> >> DnaA;protein_id=YP_479125.1;db_xref=GI: 
> 86738725 
> ;db_xref 
> = 
> InterPro:IPR001957 
> ;db_xref 
> = 
> InterPro:IPR003593 
> ;db_xref 
> =InterPro:IPR013159;db_xref=InterPro:IPR013317;db_xref=GeneID: 
> 3902947;exon_number=1
> >>
> >> While there is not anything technically wrong with these two lines,
> >> there is what you might call a logic error: the CDS should have the
> >> gene as a parent.  Without that information, a genome browser is  
> going
> >> to have a difficult time displaying the data appropriately.  Feel  
> free
> >> to complain to the folks at NCBI that there GFF3 is really bad  
> (I've
> >> done that a few times, but I think they are ignoring me :-)
> >>
> >> So, the question is, what should you use?  The best option I can
> >> suggest to you is the genbank2gff3 script that comes with BioPerl,
> >> called bp_genbank2gff3.pl. If you get the developers version from
> >> github, you can use a version of that script that has been fixed to
> >> work appropriately with bacterial/circular genomes.
> >>
> >> Scott
> >>
> >>
> >> On Fri, Jul 23, 2010 at 10:54 AM, David Breimann
> >> <dav...@gm...> wrote:
> >>> I am trying to set up my first genome, after successfully  
> playing with
> >>> the tutorial examples. and I run into some problems.
> >>>
> >>> I use a fasta and a gff file from NCBI:
> >>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
> >>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
> >>>
> >>> Setting up the sequence file seems to pass OK, but when I run
> >>> flatfile-to-json.pl with the GFF I get an error:
> >>>
> >>>
> >>> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
> >>> --tracklabel test -key test
> >>>
> >>> working on seq gi|86738724|ref|NC_007777.1|
> >>> Use of uninitialized value in string eq at
> >>> ../../../jbrowse/bin/flatfile-to-json.pl line 179, <GEN2> line 24.
> >>>
> >>> What's wrong?
> >>>
> >>> Thank you,
> >>> David
> >>>
> >>>
> >>>  
> ------------------------------------------------------------------------------
> >>> This SF.net email is sponsored by Sprint
> >>> What will you do first with EVO, the first 4G phone?
> >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> >>> _______________________________________________
> >>> Gmod-ajax mailing list
> >>> Gmo...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>>
> >>
> >>
> >>
> >> --
> >>  
> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at  
> scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                      
> 216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://ad.doubleclick.net/clk;226879339;13503038;l?
> http://clk.atdmt.com/CRS/go/247765532/direct/01/_______________________________________________
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Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Mitch S. <mit...@be...>]

Most of these are pretty high on the to-do list; specifically:

On 07/26/2010 11:24 PM, David Breimann wrote:
> 1. I would like to display some annotations from a GFF file on a 
> single track and control their color/glyph according to the content of 
> the note in the GFF (e.g. if 'Note=red' I would like this feature to 
> be colored red, and if 'Note=green' I would like it to be green).

Adding an option for javascript callbacks to customize feature elements 
is on the to-do list.  The way I'm currently envisioning it, you'd be 
able to specify a javascript function that would get the HTML element 
for the feature, and the feature data (including "Note" if you specified 
it in extraData).  Then you'd be able to modify that HTML element 
however you wanted based on that data.

> 2. Can  I control for the height of the tracks (I know it can be done 
> for WIG tracks, but what about normal features tracks)?

Are you seeing tracks that are too tall, or too short, or both?

On the development branch, the density histograms now have a height 
limit.  On the other hand, if the individual features are shown there's 
currently no mechanism for limiting the height of the track, although 
that's also on the to-do list.

> 3. How can I control which tracks are shown by default?

In index.html, there's a section that looks like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback
                                });

the "defaultTracks" setting is a comma-separated list of track labels; 
those tracks will be shown by default.

> 4. Suggestion: have a "reset view" in the browser (currently I have to 
> clear my browser history to return to the default view).

I don't doubt that this is useful for you, but since I don't think I've 
heard this requested before, I'm interested in the specifics of the use 
case.  What's the context where you want to do this?  And when you want 
to go back to the default view, what makes the default better than what 
you were looking at before?

For example, you might have two biological questions that you want to 
investigate, and each of them might be addressed using a different set 
of tracks.  So if you're looking at a bunch of tracks, and you decide 
you want to switch all those tracks off and go look at a different set 
of tracks, then that's one situation where I can imagine wanting to do 
have a "reset view" option.  But I'd like to hear the specifics of your 
case.

> 5. Is there any ETA for the improvement of the WIG tracks (most 
> importantly adding a scale)?

That's definitely high on the to-do list, but it's tough to estimate a 
time, because it'll involve restructuring the code a bit.  And I'm 
currently in the middle of dealing with another issue.  But the scale 
bar is probably first on the list after this current bug I'm working on.

Mitch

Re: [Gmod-ajax] working with a config file

[Mitch S. <mit...@be...>]

Have you looked at docs/tutorial/conf_files/volvox.json?

It uses the "memory" adaptor, which loads the files in the specified 
directory into memory and makes those available to the JBrowse code.  
That works fine if you have relatively small gff and fasta files.  Look 
at the "db_args" setting for an example of how to specify the directory, 
and at the bioperl documentation for Bio::DB::SeqFeature::Store::memory 
for more details.

If you have larger files, and if you're only using them with JBrowse 
and/or GBrowse, then the Bio::DB::SeqFeature::Store adaptor with a 
database is useful; that's how I've been setting up the Dmel demo.  
Setting up the database is more complex, though; I wrote down the steps 
I take to set up the Dmel demo here:

http://sourceforge.net/mailarchive/forum.php?thread_name=4AC20FFC.7010605%40berkeley.edu&forum_name=gmod-ajax

If you're using the database with other GMOD tools then you can also use 
the Bio::DB::Das::Chado adaptor; if you google for it, you'll find the 
documentation for setting it up.  If you run into specific problems with 
it then we can probably help.

You can indeed load the sequence using a config file; prepare-refseqs.pl 
can take a config file as an argument.  When you do that, you also have 
to specify a list of reference sequence names or IDs.  The 
prepare-refseqs.pl usage message has some details.

Even if you use a config file for the sequence and feature data, that 
doesn't change how you process the wig data; you still use wig-to-json.pl.

Mitch

On 07/26/2010 06:17 AM, David Breimann wrote:
> Hi,
>
> I use flat files (fasta, gff and wig) to build my JBrowse genomes. I 
> wnat to start using configure files, but I'm not sure how to do that. 
> Which db_adaptor should I use? Can I load the sequence file using the 
> config also or only the tracks? What about the wig? How should I 
> specify dir/file names?
>
> I has a look at 
> http://jbrowse.org/code/jbrowse-master/docs/config.html but didn't get it.
>
> Thanks,
> Dave
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
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>    

[Gmod-ajax] Formatting using GFF notes and some other stuff

[David B. <dav...@gm...>]

Hi,

1. I would like to display some annotations from a GFF file on a single
track and control their color/glyph according to the content of the note in
the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
if 'Note=green' I would like it to be green).
2. Can  I control for the height of the tracks (I know it can be done for
WIG tracks, but what about normal features tracks)?
3. How can I control which tracks are shown by default?
4. Suggestion: have a "reset view" in the browser (currently I have to clear
my browser history to return to the default view).
5. Is there any ETA for the improvement of the WIG tracks (most importantly
adding a scale)?

Keep up the good work,
Dave

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[David B. <dav...@gm...>]

Hi again guys,

Here is a example:
NC_006578.gbk from
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_thuringiensis_konkukian/NC_006578.gbkhas
a gene that spans join(77090..77112,1..586) and it produces an error:

$ bp_genbank2gff3.pl -y NC_006578.gbk
# Input: NC_006578.gbk
# working on region:NC_006578, Bacillus thuringiensis serovar konkukian str.
97-27, 23-JUL-2008, Bacillus thuringiensis serovar konkukian str. 97-27
plasmid pBT9727, complete sequence.
NC_006578 Unflattening error:
Details:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: PROBLEM, SEVERITY==2
Ranges not in correct order. Strange ensembl genbank entry? Range:
[77090,77112] [1,586]
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:473
STACK: Bio::SeqFeature::Tools::Unflattener::problem
/usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:952
STACK: Bio::SeqFeature::Tools::Unflattener::_check_order_is_consistent
/usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2842
STACK: Bio::SeqFeature::Tools::Unflattener::infer_mRNA_from_CDS
/usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:2713
STACK: Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/share/perl/5.10.1/Bio/SeqFeature/Tools/Unflattener.pm:1532
STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:1023
STACK: /usr/local/bin/bp_genbank2gff3.pl:506
-----------------------------------------------------------

# Possible gene unflattening error withNC_006578: consult STDERR
# GFF3 saved to ./NC_006578.gff; DNA saved to ./NC_006578.fa

Another similar example: NC_008785.gbk from
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Burkholderia_mallei_SAVP1/NC_008785.gbk
.

Best,
Dave


On Mon, Jul 26, 2010 at 6:20 PM, Scott Cain <sc...@sc...> wrote:

> Hi Dave,
>
> Please keep your responses on the list so they can be archived.
>
> I'm also cc'ing Nathan Liles, who did the work on the genbank2gff3
> script to deal with bacterial genomes.  Perhaps Nathan can take a look
> at this genbank entry and see more quickly what the problem is.
>
> Thanks,
> Scott
>
>
>
>
> On Sun, Jul 25, 2010 at 8:26 AM, David Breimann
> <dav...@gm...> wrote:
> > Scott,
> >
> > I cloned the latest version of bioperl from github (I'm not sure what you
> > mean by developers version; I thought the dev branch is obsolete but I'm
> not
> > sure; anyway - I got the version from bioperl-live).
> > bp_genbank2gff3.pl fails exactly on features which are on the margin,
> e.g.
> > "Ranges not in correct order. Strange ensembl genbank entry? Range:
> > [207497,208369] [1,687]".
> >
> > Thanks,
> > Dave
> >
> > On Fri, Jul 23, 2010 at 6:10 PM, Scott Cain <sc...@sc...> wrote:
> >> Hi David,
> >>
> >> The NCBI GFF3 is notoriously bad and doesn't pass validation at the
> >> GFF3 validator:
> >>
> >>  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
> >>
> >> The most notable problems actually have to do with the relationships
> >> between features.  For example, in the first few lines:
> >>
> >> NC_007777.1     RefSeq  gene    35      1723    .       +       .
> >>  locus_tag=Francci3_0001;db_xref=GeneID:3902947
> >> NC_007777.1     RefSeq  CDS     35      1720    .       +       0
> >>  locus_tag=Francci3_0001;transl_table=11;product=chromosomal
> >> replication initiator protein
> >>
> >>
> DnaA;protein_id=YP_479125.1;db_xref=GI:86738725;db_xref=InterPro:IPR001957;db_xref=InterPro:IPR003593;db_xref=InterPro:IPR013159;db_xref=InterPro:IPR013317;db_xref=GeneID:3902947;exon_number=1
> >>
> >> While there is not anything technically wrong with these two lines,
> >> there is what you might call a logic error: the CDS should have the
> >> gene as a parent.  Without that information, a genome browser is going
> >> to have a difficult time displaying the data appropriately.  Feel free
> >> to complain to the folks at NCBI that there GFF3 is really bad (I've
> >> done that a few times, but I think they are ignoring me :-)
> >>
> >> So, the question is, what should you use?  The best option I can
> >> suggest to you is the genbank2gff3 script that comes with BioPerl,
> >> called bp_genbank2gff3.pl. If you get the developers version from
> >> github, you can use a version of that script that has been fixed to
> >> work appropriately with bacterial/circular genomes.
> >>
> >> Scott
> >>
> >>
> >> On Fri, Jul 23, 2010 at 10:54 AM, David Breimann
> >> <dav...@gm...> wrote:
> >>> I am trying to set up my first genome, after successfully playing with
> >>> the tutorial examples. and I run into some problems.
> >>>
> >>> I use a fasta and a gff file from NCBI:
> >>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
> >>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
> >>>
> >>> Setting up the sequence file seems to pass OK, but when I run
> >>> flatfile-to-json.pl with the GFF I get an error:
> >>>
> >>>
> >>> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
> >>> --tracklabel test -key test
> >>>
> >>> working on seq gi|86738724|ref|NC_007777.1|
> >>> Use of uninitialized value in string eq at
> >>> ../../../jbrowse/bin/flatfile-to-json.pl line 179, <GEN2> line 24.
> >>>
> >>> What's wrong?
> >>>
> >>> Thank you,
> >>> David
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> This SF.net email is sponsored by Sprint
> >>> What will you do first with EVO, the first 4G phone?
> >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> >>> _______________________________________________
> >>> Gmod-ajax mailing list
> >>> Gmo...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>>
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[Scott C. <sc...@sc...>]

Hi Dave,

Please keep your responses on the list so they can be archived.

I'm also cc'ing Nathan Liles, who did the work on the genbank2gff3
script to deal with bacterial genomes.  Perhaps Nathan can take a look
at this genbank entry and see more quickly what the problem is.

Thanks,
Scott




On Sun, Jul 25, 2010 at 8:26 AM, David Breimann
<dav...@gm...> wrote:
> Scott,
>
> I cloned the latest version of bioperl from github (I'm not sure what you
> mean by developers version; I thought the dev branch is obsolete but I'm not
> sure; anyway - I got the version from bioperl-live).
> bp_genbank2gff3.pl fails exactly on features which are on the margin, e.g.
> "Ranges not in correct order. Strange ensembl genbank entry? Range:
> [207497,208369] [1,687]".
>
> Thanks,
> Dave
>
> On Fri, Jul 23, 2010 at 6:10 PM, Scott Cain <sc...@sc...> wrote:
>> Hi David,
>>
>> The NCBI GFF3 is notoriously bad and doesn't pass validation at the
>> GFF3 validator:
>>
>>  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>>
>> The most notable problems actually have to do with the relationships
>> between features.  For example, in the first few lines:
>>
>> NC_007777.1     RefSeq  gene    35      1723    .       +       .
>>  locus_tag=Francci3_0001;db_xref=GeneID:3902947
>> NC_007777.1     RefSeq  CDS     35      1720    .       +       0
>>  locus_tag=Francci3_0001;transl_table=11;product=chromosomal
>> replication initiator protein
>>
>> DnaA;protein_id=YP_479125.1;db_xref=GI:86738725;db_xref=InterPro:IPR001957;db_xref=InterPro:IPR003593;db_xref=InterPro:IPR013159;db_xref=InterPro:IPR013317;db_xref=GeneID:3902947;exon_number=1
>>
>> While there is not anything technically wrong with these two lines,
>> there is what you might call a logic error: the CDS should have the
>> gene as a parent.  Without that information, a genome browser is going
>> to have a difficult time displaying the data appropriately.  Feel free
>> to complain to the folks at NCBI that there GFF3 is really bad (I've
>> done that a few times, but I think they are ignoring me :-)
>>
>> So, the question is, what should you use?  The best option I can
>> suggest to you is the genbank2gff3 script that comes with BioPerl,
>> called bp_genbank2gff3.pl. If you get the developers version from
>> github, you can use a version of that script that has been fixed to
>> work appropriately with bacterial/circular genomes.
>>
>> Scott
>>
>>
>> On Fri, Jul 23, 2010 at 10:54 AM, David Breimann
>> <dav...@gm...> wrote:
>>> I am trying to set up my first genome, after successfully playing with
>>> the tutorial examples. and I run into some problems.
>>>
>>> I use a fasta and a gff file from NCBI:
>>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
>>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
>>>
>>> Setting up the sequence file seems to pass OK, but when I run
>>> flatfile-to-json.pl with the GFF I get an error:
>>>
>>>
>>> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
>>> --tracklabel test -key test
>>>
>>> working on seq gi|86738724|ref|NC_007777.1|
>>> Use of uninitialized value in string eq at
>>> ../../../jbrowse/bin/flatfile-to-json.pl line 179, <GEN2> line 24.
>>>
>>> What's wrong?
>>>
>>> Thank you,
>>> David
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>



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

[Gmod-ajax] working with a config file

[David B. <dav...@gm...>]

Hi,

I use flat files (fasta, gff and wig) to build my JBrowse genomes. I wnat to
start using configure files, but I'm not sure how to do that. Which
db_adaptor should I use? Can I load the sequence file using the config also
or only the tracks? What about the wig? How should I specify dir/file names?

I has a look at http://jbrowse.org/code/jbrowse-master/docs/config.html but
didn't get it.

Thanks,
Dave

Re: [Gmod-ajax] safe way to delete some of the tracks?

[Ian H. <ih...@be...>]

Here's the ticket:

http://jbrowse.lighthouseapp.com/projects/23792/tickets/53-script-to-remove-tracks

David Breimann wrote:
> Hello,
> 
> I use JBrowse with a number of different genomes. For each genome,
> there is obiovusly its sequence (fasta fil) and an annotaion file
> (GFF3). Now every now and then I add some track and then want to
> remove them, but without deleting the entire directory so that I won't
> have to set the sequence and main GFF again.
> Is that possible? That is, neatly remove just some of the tracks?
> 
> Thanks,
> David
> 
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] safe way to delete some of the tracks?

[Ian H. <ih...@be...>]

For now the easiest way is to manually delete from data/trackInfo.js the 
clause corresponding to this track. This means deleting a brace-enclosed 
block like this:

    {
       "url" : "data/tracks/{refseq}/EnsemblGenes/trackData.json",
       "type" : "FeatureTrack",
       "label" : "EnsemblGenes",
       "key" : "Ensembl Genes"
    },


A little utility to do this would be straightforward to write and has 
been one of our to-dos for a while. Feel free to beat us to it & write 
one yourself :)

Cheers
Ian


David Breimann wrote:
> Hello,
> 
> I use JBrowse with a number of different genomes. For each genome,
> there is obiovusly its sequence (fasta fil) and an annotaion file
> (GFF3). Now every now and then I add some track and then want to
> remove them, but without deleting the entire directory so that I won't
> have to set the sequence and main GFF again.
> Is that possible? That is, neatly remove just some of the tracks?
> 
> Thanks,
> David
> 
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] bin/wig2png missing?

[Ian H. <ih...@be...>]

Glad you got this working, David. I think if you use 'configure' prior to make, it should pick up the libpng version discrepancy, though I'd have to check that.



On Jul 25, 2010, at 7:35 AM, David Breimann <dav...@gm...> wrote:

> but not libpng12-dev. installing it solved the problem. I guess I missed this part in the tutorial. sorry!
> 
> On Sun, Jul 25, 2010 at 5:28 PM, David Breimann <dav...@gm...> wrote:
> p.s. I have libpng 1.2.42 installed on my system.
> 
> 
> On Sun, Jul 25, 2010 at 5:21 PM, David Breimann <dav...@gm...> wrote:
> Hi,
> 
> I just cloned JBrowse on a clean machine. everthing seemed to work fine, but when I tried adding a wig file using bin/wig-to-json.pl, I got the following error:
> 
> Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing 'make' in jbrowse root directory?) at bin/wig-to-json.pl line 26.
> 
> Indeed, bin/wig2png is missing from bin/. I tried the make suggestion but it resulted in an error:
> g++ -I/usr/X11/include -include src/config.h -L/usr/X11/lib -lpng  -o bin/wig2png src/wig2png.cc src/opts_list.cc
> src/wig2png.cc:24:17: error: png.h: No such file or directory
> src/wig2png.cc:40: error: ‘png_bytep’ has not been declared
> src/wig2png.cc:40: error: ‘png_color’ has not been declared
> src/wig2png.cc: In function ‘void write_png_file(const char*, int, int, int*, int*, int, int)’:
> ... and so on.
> 
> I tried a fresh clone but again wig2png is missing.
> 
> p.s.
> I clone using http://github...
> instead git://github due to some port restrictions in my university.
> 
> Thanks,
> Dave
> 
> 
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] bin/wig2png missing?

[David B. <dav...@gm...>]

but not libpng12-dev. installing it solved the problem. I guess I missed
this part in the tutorial. sorry!

On Sun, Jul 25, 2010 at 5:28 PM, David Breimann <dav...@gm...>wrote:

> p.s. I have libpng 1.2.42 installed on my system.
>
>
> On Sun, Jul 25, 2010 at 5:21 PM, David Breimann <dav...@gm...>wrote:
>
>> Hi,
>>
>> I just cloned JBrowse on a clean machine. everthing seemed to work fine,
>> but when I tried adding a wig file using bin/wig-to-json.pl, I got the
>> following error:
>>
>> Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing
>> 'make' in jbrowse root directory?) at bin/wig-to-json.pl line 26.
>>
>> Indeed, bin/wig2png is missing from bin/. I tried the make suggestion but
>> it resulted in an error:
>> g++ -I/usr/X11/include -include src/config.h -L/usr/X11/lib -lpng  -o
>> bin/wig2png src/wig2png.cc src/opts_list.cc
>> src/wig2png.cc:24:17: error: png.h: No such file or directory
>> src/wig2png.cc:40: error: ‘png_bytep’ has not been declared
>> src/wig2png.cc:40: error: ‘png_color’ has not been declared
>> src/wig2png.cc: In function ‘void write_png_file(const char*, int, int,
>> int*, int*, int, int)’:
>> ... and so on.
>>
>> I tried a fresh clone but again wig2png is missing.
>>
>> p.s.
>> I clone using http://github...
>> instead git://github due to some port restrictions in my university.
>>
>> Thanks,
>> Dave
>>
>
>

Re: [Gmod-ajax] bin/wig2png missing?

[David B. <dav...@gm...>]

p.s. I have libpng 1.2.42 installed on my system.

On Sun, Jul 25, 2010 at 5:21 PM, David Breimann <dav...@gm...>wrote:

> Hi,
>
> I just cloned JBrowse on a clean machine. everthing seemed to work fine,
> but when I tried adding a wig file using bin/wig-to-json.pl, I got the
> following error:
>
> Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing
> 'make' in jbrowse root directory?) at bin/wig-to-json.pl line 26.
>
> Indeed, bin/wig2png is missing from bin/. I tried the make suggestion but
> it resulted in an error:
> g++ -I/usr/X11/include -include src/config.h -L/usr/X11/lib -lpng  -o
> bin/wig2png src/wig2png.cc src/opts_list.cc
> src/wig2png.cc:24:17: error: png.h: No such file or directory
> src/wig2png.cc:40: error: ‘png_bytep’ has not been declared
> src/wig2png.cc:40: error: ‘png_color’ has not been declared
> src/wig2png.cc: In function ‘void write_png_file(const char*, int, int,
> int*, int*, int, int)’:
> ... and so on.
>
> I tried a fresh clone but again wig2png is missing.
>
> p.s.
> I clone using http://github...
> instead git://github due to some port restrictions in my university.
>
> Thanks,
> Dave
>

[Gmod-ajax] bin/wig2png missing?

[David B. <dav...@gm...>]

Hi,

I just cloned JBrowse on a clean machine. everthing seemed to work fine, but
when I tried adding a wig file using bin/wig-to-json.pl, I got the following
error:

Can't find binary executable /var/www/jbrowse/bin/wig2png (try typing 'make'
in jbrowse root directory?) at bin/wig-to-json.pl line 26.

Indeed, bin/wig2png is missing from bin/. I tried the make suggestion but it
resulted in an error:
g++ -I/usr/X11/include -include src/config.h -L/usr/X11/lib -lpng  -o
bin/wig2png src/wig2png.cc src/opts_list.cc
src/wig2png.cc:24:17: error: png.h: No such file or directory
src/wig2png.cc:40: error: ‘png_bytep’ has not been declared
src/wig2png.cc:40: error: ‘png_color’ has not been declared
src/wig2png.cc: In function ‘void write_png_file(const char*, int, int,
int*, int*, int, int)’:
... and so on.

I tried a fresh clone but again wig2png is missing.

p.s.
I clone using http://github...
instead git://github due to some port restrictions in my university.

Thanks,
Dave

[Gmod-ajax] safe way to delete some of the tracks?

[David B. <dav...@gm...>]

Hello,

I use JBrowse with a number of different genomes. For each genome,
there is obiovusly its sequence (fasta fil) and an annotaion file
(GFF3). Now every now and then I add some track and then want to
remove them, but without deleting the entire directory so that I won't
have to set the sequence and main GFF again.
Is that possible? That is, neatly remove just some of the tracks?

Thanks,
David

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[David B. <dav...@gm...>]

Thank you Scott and Mitch!

On Fri, Jul 23, 2010 at 6:25 PM, Mitch Skinner
<mit...@be...> wrote:
> This one is usually the result of a previous flatfile-to-json.pl or
> biodb-to-json.pl run that didn't specify a track label.
>
> Look in data/trackInfo.js for an entry that doesn't have a "label"
> attribute.  Entries are supposed to look something like this:
>
>   {
>      "url" : "data/tracks/{refseq}/gene/trackData.json",
>      "label" : "gene",
>      "type" : "FeatureTrack",
>      "key" : "Gene"
>   },
>
> but if "label" is missing then you'll see that error message.
>
> I thought I added a check that would give a nicer error if the user forgets
> to specify a label, but that might have been only on the development branch.
>  I'll check again.
>
> Mitch
>
> On 07/23/2010 07:54 AM, David Breimann wrote:
>>
>> I am trying to set up my first genome, after successfully playing with
>> the tutorial examples. and I run into some problems.
>>
>> I use a fasta and a gff file from NCBI:
>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
>>
>> Setting up the sequence file seems to pass OK, but when I run
>> flatfile-to-json.pl with the GFF I get an error:
>>
>>
>> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
>> --tracklabel test -key test
>>
>> working on seq gi|86738724|ref|NC_007777.1|
>> Use of uninitialized value in string eq at
>> ../../../jbrowse/bin/flatfile-to-json.pl line 179,<GEN2>  line 24.
>>
>> What's wrong?
>>
>> Thank you,
>> David
>>
>>
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>
>

Re: [Gmod-ajax] Define boundary in DNA Fasta sequence

[Mitch S. <mit...@be...>]

On 07/22/2010 12:06 PM, Swapnil Nagar wrote:
> I have successfully put the DNA sequence in the Jbrowse. We were hoping that like we define the gene boundary for Mrna, Can we do same for the DNA (fasta sequence)? It would be really nice if jbrowse enable us to highlight the biological classes(5' UTR, 3'UTR, exon, intron, etc) in different color.
>    

I'm sorry, but I don't understand what you're asking.  Are you talking 
about adding some sort of highlighting to the DNA track?  If that's the 
case, I don't see how that would work since there's (currently) only one 
DNA track but there can be multiple distinct overlapping mRNAs with 
differing definitions of what regions are UTRs or exons or introns.  
Your lab works with eukaryotes, right?

Or maybe you have something entirely different in mind?  Could you 
elaborate, and maybe give a specific example?

Mitch

Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[Mitch S. <mit...@be...>]

This one is usually the result of a previous flatfile-to-json.pl or 
biodb-to-json.pl run that didn't specify a track label.

Look in data/trackInfo.js for an entry that doesn't have a "label" 
attribute.  Entries are supposed to look something like this:

    {
       "url" : "data/tracks/{refseq}/gene/trackData.json",
       "label" : "gene",
       "type" : "FeatureTrack",
       "key" : "Gene"
    },

but if "label" is missing then you'll see that error message.

I thought I added a check that would give a nicer error if the user 
forgets to specify a label, but that might have been only on the 
development branch.  I'll check again.

Mitch

On 07/23/2010 07:54 AM, David Breimann wrote:
> I am trying to set up my first genome, after successfully playing with
> the tutorial examples. and I run into some problems.
>
> I use a fasta and a gff file from NCBI:
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
>
> Setting up the sequence file seems to pass OK, but when I run
> flatfile-to-json.pl with the GFF I get an error:
>
>
> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
> --tracklabel test -key test
>
> working on seq gi|86738724|ref|NC_007777.1|
> Use of uninitialized value in string eq at
> ../../../jbrowse/bin/flatfile-to-json.pl line 179,<GEN2>  line 24.
>
> What's wrong?
>
> Thank you,
> David
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>