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

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

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
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>> > worldwide. Take advantage of special opportunities to increase revenue
>> > and
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>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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