[BioC] DEXSeq dexseq_prepare_annotation.py error

minyoung [guest] guest at bioconductor.org
Fri Feb 22 05:00:17 CET 2013


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 

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