Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff

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

Hi Anja,

I exported your drawing as a pdf to make it more widely viewable
(though I imagine many people on this list have OpenOffice).  What you
drew is easy to display.  I was expecting that you wanted them all to
be on the same line with different icons representing the different
types of repeats, as opposed to each element being in a separate
track.

Scott


On Thu, Aug 26, 2010 at 2:45 PM, Anja Friedrich
<fri...@ho...> wrote:
> Hi Scott,
>
> I attached a little sketch (just for 1 region). I hope you can open it...
> Ithink it should be possible to display it like this in JBrowse...
> I saw that I forgott to answer your other questions. Sorry for that. Taro
> (Colocasia esculenta) is the name plant I got the squwnce from. The feature
> is called Nested Tandem Repeat (NTR).
>
> Anja
>
>> Date: Thu, 26 Aug 2010 14:33:48 -0400
>> Subject: Re: [Gmod-schema] nested tandem repeats/gff
>> From: sc...@sc...
>> To: fri...@ho...; gmo...@li...
>> CC: gmo...@li...
>>
>> Hi Anja,
>>
>> I'm cc'ing this to the JBrowse list they can chime in to.
>>
>> The wonderful thing about JBrowse is that it is quite flexible in what
>> it can display; that is also a downside, though, as it might require
>> you to create the underlying graphics if native support isn't there.
>> Since I don't really understand what you would want the image to look
>> like, would it be possible for you to create a sketch of what you want
>> to see? That would make it a lot easier to say whether what you want
>> to do is possible, easy or hard.
>>
>> Scott
>>
>>
>> On Thu, Aug 26, 2010 at 2:21 PM, Anja Friedrich
>> <fri...@ho...> wrote:
>> > Hi Scott,
>> >
>> > thanks for your explanation. I will go through it.
>> > As I told J my request to add nested_tandem_repeat to SO was accepted.
>> > My
>> > problem is that I have 3 different repeat regions with 2 motifs. I want
>> > to
>> > display the regions and the motifs in JBrowse. I was wondering how I
>> > have to
>> > create the single lines. One line for the region and 1 for each motif?
>> > For
>> > all 3 repeat regions of course... Would that work?
>> >
>> > Cheers,
>> > Anja
>> >
>> >
>> >> Date: Thu, 26 Aug 2010 14:10:58 -0400
>> >> Subject: Re: [Gmod-schema] nested tandem repeats/gff
>> >> From: sc...@sc...
>> >> To: jm...@vc...
>> >> CC: fri...@ho...; gmo...@li...
>> >>
>> >> Hi Anja,
>> >>
>> >> I'm going to put comments below in response to both you and J.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Thu, Aug 26, 2010 at 11:54 AM, J.M.P. Alves <jm...@vc...> wrote:
>> >> > Hallo,
>> >> >
>> >> > A few possibilities I see, although I am not positive they are the
>> >> > actual problem:
>> >> >
>> >> >  > 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >> >
>> >> > Are "nested_repeat" and "repeat_fragment" part of the sequence
>> >> > ontology
>> >> > vocabulary? I think you can use anything you want on the second
>> >> > column
>> >> > there ("program"), but the 3rd one is restricted.
>> >>
>> >> In my instance of Chado (a few weeks old at the most), SO has both
>> >> terms, so that isn't likely the problem, but it's a good idea to
>> >> check. A query like this would tell you if it's present:
>> >>
>> >> select cvterm.* from cvterm join cv using (cv_id)
>> >> where cv.name='sequence' and cvterm.name='nested_repeat';
>> >>
>> >> >
>> >> > NTR is the name of the sequence (as in the FASTA file), right?
>> >>
>> >> Right, if a feature named NTR isn't already in the database, you will
>> >> have problems. From the error message you are getting, I'm guessing
>> >> it's already there (or it would have complained about that), but
>> >> perhaps I misremembering the order of error messaging. I would
>> >> suggest getting rid of the sequence-region directive, as unless you
>> >> have a fairly recent checkout of bioperl-live it will cause problems,
>> >> and in any event, will never be supported for defining a feature (and
>> >> this one isn't properly formed anyway--there's no start value and "bp"
>> >> isn't part of the spec). Instead, add a full gff line:
>> >>
>> >> NTR . contig 1 5428 . . . ID=NTR;Name=NTR
>> >>
>> >> Looking at your sample GFF again, it looks to me like you want these
>> >> feature to reside on a feature called "taro", is that right? Or is
>> >> there a feature called NTR? If the contig/chromosome/whatever is
>> >> called taro, then you should replace the text in the first column of
>> >> the gff with "taro" and create a GFF line for it, like I did for NTR
>> >> above.
>> >>
>> >> >
>> >> > Another possible problem:
>> >> >
>> >> >  > 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >> >
>> >> > I don't know if this is the case, but I thought every line had to
>> >> > have
>> >> > an ID attribute, e.g.:
>> >> >
>> >> > NTR program repeat_fragment 1505 1553 . + . ID=rf1;Parent=ID1
>> >>
>> >> Not so: ID tags are only needed in two cases:
>> >>
>> >> 1. To identify a feature so it can be referred to later to show
>> >> parentage (as Anja did in the sample GFF) and
>> >>
>> >> 2. To identify a reference sequence so it can be referred to in column
>> >> one (this is NOT part of the GFF3 spec, but life will work a lot
>> >> better with Chado if reference sequences look like
>> >> "ID=chr1;Name=chr1..."
>> >>
>> >> Scott
>> >>
>> >> >
>> >> > I hope some of these ideas help.
>> >> >
>> >> > J
>> >> >
>> >> > Anja Friedrich wrote:
>> >> >> Hi all,
>> >> >>
>> >> >> not sure if my earlier mail reached, because I was texting from a
>> >> >> different e-mail.
>> >> >>
>> >> >> I tried to load nested tandem repeats into chado. As this fature
>> >> >> doesnt
>> >> >> exist yet for gff3 I tried to get around:
>> >> >>
>> >> >> 0  ##gff-version   3
>> >> >> 1  ##sequence-region   taro 5428 bp
>> >> >> 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >> >> 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >> >> 4 NTR program repeat_fragement 473 483 . + . Parent=ID1
>> >> >>
>> >> >> But I get this error message:
>> >> >>
>> >> >> anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism Taro
>> >> >>  --gfffile
>> >> >> taro.gffCommand line argument used for root
>> >> >> Preparing data for inserting into the chado database
>> >> >> (This may take a while ...)
>> >> >>
>> >> >> --------------------- WARNING ---------------------
>> >> >> MSG: Calling end without a defined start position
>> >> >> ---------------------------------------------------
>> >> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 808, <GEN0> line 1.
>> >> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 809, <GEN0> line 1.
>> >> >>
>> >> >> ------------- EXCEPTION: Bio::Root::Exception -------------
>> >> >> MSG: no cvterm for
>> >> >> STACK: Error::throw
>> >> >> STACK: Bio::Root::Root::throw
>> >> >> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
>> >> >> STACK: Bio::GMOD::DB::Adapter::get_type
>> >> >> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4579
>> >> >> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:838
>> >> >> -----------------------------------------------------------
>> >> >>
>> >> >> Someone an idea? Cant I add the feature like this?
>> >> >>
>> >> >> Cheers,
>> >> >> Anja
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >>
>> >> >>
>> >> >>
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>> >> >> _______________________________________________
>> >> >> Gmod-schema mailing list
>> >> >> Gmo...@li...
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >> > --
>> >> > -------------------------------
>> >> > João Marcelo Pereira Alves (J)
>> >> > Post-doctoral fellow
>> >> > MCV / VCU - Richmond, VA
>> >> > http://bioinfo.lpb.mic.vcu.edu
>> >> > f. 1-804-828-3897
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> >> > Be part of this innovative community and reach millions of netbook
>> >> > users
>> >> > worldwide. Take advantage of special opportunities to increase
>> >> > revenue
>> >> > and
>> >> > speed time-to-market. Join now, and jumpstart your future.
>> >> > http://p.sf.net/sfu/intel-atom-d2d
>> >> > _______________________________________________
>> >> > Gmod-schema mailing list
>> >> > Gmo...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> 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
>



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