[BioC] rtracklayer: No export function for 'bedLines' found [was Re: intermittent oddity in rtracklayer track names]

[Paul Shannon]

Hi Michael,

strand = '*' solves the 'm' and 'p' suffixes. Thanks.

This leads to another oddity.  When I expand my GRange -- the one passed to broserView -- to include all of chromosome 1, I get this error:

   Error in .exportForFormat(format) :
     No export function for 'bedLines' found

I find -- loosely speaking -- that this error comes up whenever I ask to view more than half of chromosome one.

I report this in the same (possibly unclarifying) was as the 'm' and 'p' report.  That is, I don't have a small reproducible example.  Maybe you can recognize the problem from my short description instead.

Thanks,

 - Paul

On Oct 25, 2010, at 10:16 PM, Michael Lawrence wrote:

> 
> 
> On Mon, Oct 25, 2010 at 1:33 PM, Paul Shannon <pshannon at systemsbiology.org> wrote:
> I've tried hard to come up with a minimal example of this -- some fragment of code to reproduce the error -- but I haven't figured out yet how to do that.  So instead, and thinking that a brief report might be useful, and will possibly trigger something in Michael's mind, I send this narrative email instead.
> 
> I create a track with this command:
> 
>   track (session, 'exonHits') = grange   # a GRangesForUCSCGenome object
> 
> Then I ask to look at the track:
> 
>   view <- browserView (session, range.to.view, full='exonHits', dense='ruler', hide=trackNames (session))
> 
> The problem is that sometimes I get this error:
> 
>   Error in resolveTrackIndex(x, i) : Unknown track(s): exonHits
> 
> When I look for the 'exonHits' track, I learn that there are actually two of them, each with a suffix:  "exonHits m" and "exonHits p"
> 
>    > grep ('exonHits',  trackNames (session.sub), ignore.case=T, v=T)
>             exonHits m          exonHits p
>     "ct_exonHitsm_7841" "ct_exonHitsp_7844"
> 
> I can use these odd, modified track names, and display the desired:
> 
>   view <- browserView (session, range.to.view, full='exonHits m', dense='ruler', hide=trackNames (session))
> 
> But it seems rather suspicious.  Is there any reason for the 'm' and 'p' suffixes?
> 
> 
> You've caught another undocumented feature. The graph formats like  "wig" or "bedGraph" do not encode a strand. Since UCSC supports multiple tracks, if values come from multiple strands, we split them up, for the (m)inus and (p)lus strands. If this is not desirable, just set the strand on all features to "*".
>  
> Thanks,
> 
>  - Paul
> 
> 
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