Hi,

I am trying to prepare my data for DEXSeq with the python script provided by the package.

I have downloaded the file from here. it is a gff file of considerable size (over 2Gb when unzipped).

wget ftp://flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-r6.03.gff.gz
gunzip dmel-all-r6.03.gff.gz
mv dmel-all-r6.03.gff.gz Dmel_r6.03.gff
python  ~/R/x86_64-pc-linux-gnu-library/3.1/DEXSeq/python_scripts/dexseq_prepare_annotation.py Dmel_r6.03.gff gffFiles/Dmel.DEXSeq.r6.03.gtf

When I try to run the python script to convert it to a DEXSeq-friendly format I get the error message:

Traceback (most recent call last):
  File "/home/yeroslaviz/R/x86_64-pc-linux-gnu-library/3.1/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 54, in <module>
    f.attr['gene_id'] = f.attr['gene_id'].replace( ":", "_" )
KeyError: 'gene_id'

Is there a way to make DEXSeq works with this file?

Assa

sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] DEXSeq_1.12.1           BiocParallel_1.0.0      DESeq2_1.6.1           
 [4] RcppArmadillo_0.4.500.0 Rcpp_0.11.3             GenomicRanges_1.18.1   
 [7] GenomeInfoDb_1.2.3      IRanges_2.0.0           S4Vectors_0.4.0        
[10] Biobase_2.26.0          BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.44.0      AnnotationDbi_1.28.1
 [4] base64enc_0.1-2      BatchJobs_1.5        BBmisc_1.8          
 [7] biomaRt_2.22.0       Biostrings_2.34.0    bitops_1.0-6        
[10] brew_1.0-6           checkmate_1.5.0      cluster_1.15.3      
[13] codetools_0.2-9      colorspace_1.2-4     DBI_0.3.1           
[16] digest_0.6.4         fail_1.2             foreach_1.4.2       
[19] foreign_0.8-61       Formula_1.1-2        genefilter_1.48.1   
[22] geneplotter_1.44.0   ggplot2_1.0.0        grid_3.1.0          
[25] gtable_0.1.2         Hmisc_3.14-5         hwriter_1.3.2       
[28] iterators_1.0.7      lattice_0.20-29      latticeExtra_0.6-26
[31] locfit_1.5-9.1       MASS_7.3-35          munsell_0.4.2       
[34] nnet_7.3-8           plyr_1.8.1           proto_0.3-10        
[37] RColorBrewer_1.0-5   RCurl_1.95-4.3       reshape2_1.4        
[40] rpart_4.1-8          Rsamtools_1.18.2     RSQLite_1.0.0       
[43] scales_0.2.4         sendmailR_1.2-1      splines_3.1.0       
[46] statmod_1.4.20       stringr_0.6.2        survival_2.37-7     
[49] tools_3.1.0          XML_3.98-1.1         xtable_1.7-4        
[52] XVector_0.6.0        zlibbioc_1.12.0