[BioC] DEXSeq dexseq_prepare_annotation.py error

[Simon Anders]

Hi

On 22/02/13 05:00, minyoung [guest] wrote:
> IndexError: Cannot subset to zero-length interval.

Thanks for reporting this; the error arose due to a change to HTSeq that 
I did when I released the new version 0.5.4 yesterday. (Alejandro 
probably hasn't updated yet, this is why he could not reproduce it.)

I have just fixed the issue and uploaded patch version 0.5.4p1. Please 
try with that one.

If you are curious: There is some confusion on whether the intervals 
given in a GFF file end on the last base-pair or reach one beyond it. 
(The GFF2 and GTF spec says the fomer, the GFF3 spec the latter.) I 
toggled the default in HTSeq and messed it up. Your GTF file contains 
one curious exon that is only one base pair long, and the bug I 
introduced let it appear as a length-zero feature.

   Simon