[Genome] GTF custom track problem ..

[Benjamin Berman]

Hi there,

I'm having another problem with custom tracks, I don't know if it's a  
bug or just confusing documentation.

When I put the following GTF file into the custom tracks page, it  
works great:

chr8    hg18_ct_UserTrack       exon    121000000        
121010000       1000.000000     +       .        
gene_id	"gene_idREGION1"; transcript_id "gene_idREGION1";

But when I remove the "transcript_id" attribute, it chokes:

chr8    hg18_ct_UserTrack       exon    121000000        
121010000       1000.000000     +       .       gene_id  
"gene_idREGION1";


Unfortunately, it doesn't choke gracefully.  It doesn't say that  
there's an error parsing the file, or anything like that.  It goes  
back to the "Manage Custom Tracks" page, and it looks like it was  
successfully read in, but the track line has no "Items" or "Pos"  
columns as it normally does (I'm attaching a screenshot).  The track  
actually doesn't register at all; for instance, if you go to the  
table manager it's simply not there.

I went to the GTF2 specification page, it looks like maybe both the  
"gene_id" and "transcript_id" attributes are mandatory for valid  
GTF.  I'm not totally sure.  But your formats page says that they are  
just "examples" of attributes one can use, it doesn't say anything  
about them being mandatory.

Anyway, i hope you could change the parser so it at least complains  
correctly if you enter a GTF without the correct format.  This should  
save people frustration :)  You could also change your documentation  
page if it doesn't accurately reflect the GTF requirements.

Thanks!

ben.


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Ben Berman, PhD
Postdoctoral Fellow, Preventive Medicine
Keck School of Medicine of USC
1441 Eastlake Ave., Rm NOR 4423
Los Angeles, CA 90033