[BioC] DEXSeq dexseq_prepare_annotation.py error
Simon Anders
anders at embl.de
Fri Feb 22 10:13:43 CET 2013
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
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