FFF multiple sequence ID issue

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

FFF multiple sequence ID issue

Vladimir Gritsenko
Hello all,

I’m having a problem with an FFF file. It defines an xyplot histogram, and includes multiple sequence IDs. However, GBrowse 2.49 (as deployed on CGD) files all features under the first sequence ID it encounters, and ignored the rest.

This leads to me another question. Is there a “canonical" version of GBrowse against which potential bugs can be tested?

The test data is:

[CNV]
glyph = xyplot
graph_type=histogram
fgcolor = black
bgcolor = black
height=50
min_score=0
max_score=4
label=1
key=CNV histogram

CNV " " Ca21chr1_C_albicans_SC5314:1..5000 score=4

CNV " " Ca21chr2_C_albicans_SC5314:1..5000 score=3

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: FFF multiple sequence ID issue

Vladimir Gritsenko
In case anyone else runs into this, my solution was to switch to GFF3. One potential issue to resolve is aggregation - every data point will be its own plot, flooding the track with axes. The solution is to aggregate all the desired data points under the same ID, so it looks something like this:

Ca22chrRA_C_albicans_SC5314 Ymap CNV 81 100 2.5 . . ID=C1
Ca22chrRA_C_albicans_SC5314 Ymap CNV 101 120 2.5 . . ID=C1

Ca22chr1A_C_albicans_SC5314 Ymap CNV 20 40 2 . . ID=C2
Ca22chr1A_C_albicans_SC5314 Ymap CNV 41 60 1 . . ID=C2

> On Feb 25, 2015, at 6:28 PM, Vladimir Gritsenko <[hidden email]> wrote:
>
> Hello all,
>
> I’m having a problem with an FFF file. It defines an xyplot histogram, and includes multiple sequence IDs. However, GBrowse 2.49 (as deployed on CGD) files all features under the first sequence ID it encounters, and ignored the rest.
>
> This leads to me another question. Is there a “canonical" version of GBrowse against which potential bugs can be tested?
>
> The test data is:
>
> [CNV]
> glyph = xyplot
> graph_type=histogram
> fgcolor = black
> bgcolor = black
> height=50
> min_score=0
> max_score=4
> label=1
> key=CNV histogram
>
> CNV " " Ca21chr1_C_albicans_SC5314:1..5000 score=4
>
> CNV " " Ca21chr2_C_albicans_SC5314:1..5000 score=3


------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse