[BioC] DEXSeq dexseq_prepare_annotation.py error

[Alejandro Reyes]

Hello,

I was unable to reproduce your error, for me the script worked as 
expected without any error.
What version of HTSeq are you using?

Alejandro


> Hello.
>
> When I followed examples in pasilla package documentation, I met a problem at the first step.
>
> The followings are my commands and error messages:
> (python 2.6 and HTSeq-0.5.4. were installed.)
>
> wget ftp://ftp.ensembl.org/pub/release-70/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP5.70.gtf.gz
> gzip -d Drosophila_melanogaster.BDGP5.70.gtf.gz
>
> /usr/bin/python2.6 /data1/sbm/R-2.15.2/lib64/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.70.gtf Dmel.BDGP5.70.DEXSeq.chr.gff
>
> Traceback (most recent call last):
>    File "/data1/sbm/R-2.15.2/lib64/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 29, in <module>
>      exons[f.iv] += ( f.attr['gene_id'], f.attr['transcript_id'] )
>    File "_HTSeq.pyx", line 524, in HTSeq._HTSeq.GenomicArray.__getitem__ (src/_HTSeq.c:9452)
>    File "_HTSeq.pyx", line 384, in HTSeq._HTSeq.ChromVector.__getitem__ (src/_HTSeq.c:6800)
>    File "_HTSeq.pyx", line 348, in HTSeq._HTSeq.ChromVector._create_view (src/_HTSeq.c:6391)
> IndexError: Cannot subset to zero-length interval.
>
> How can I fix this problem?
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=ko_KR.euckr       LC_NUMERIC=C
>   [3] LC_TIME=ko_KR.euckr        LC_COLLATE=ko_KR.euckr
>   [5] LC_MONETARY=ko_KR.euckr    LC_MESSAGES=ko_KR.euckr
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=ko_KR.euckr LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DEXSeq_1.4.0       Biobase_2.18.0     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-3   XML_3.95-0.1   biomaRt_2.14.0 hwriter_1.3    statmod_1.4.17
> [6] stringr_0.6.2
>
> --
> Sent via the guest posting facility at bioconductor.org.