[Bioc-sig-seq] rtracklayer BUG!? import.bed pastes/prefixes 'chr' during import of SOME records

[Cook, Malcolm]

I find that rtracklayer's import.bed function is pasting the string 'chr' to SOME of my chromosome names in my bed file ( f, attached)

It is as if it is trying to rename (some) of them to (partially) agree with ucsc's naming convention.

I would expect import.bed  to preserve column 1 as the name of the 'space', but it does not.

But... some of the spaces have had a 'chr' prefix added!

Look at the session transcipt below!

I _think_ this behavior is NEW since I recently upgraded.

I hope not to have to revert to previous version of R / bioconductor to address this issue.

Any suggestions?

Thanks!

Malcolm Cook
Computational Biology - Stowers Institute for Medical Research




> library(rtracklayer)
Loading required package: RCurl
Loading required package: bitops
> unique(read.table('f.bed',sep="\t",skip=1)[,1])
 [1] YHet                      dmel_mitochondrion_genome
 [3] 2L                        X                        
 [5] 3L                        4                        
 [7] 2R                        3R                       
 [9] Uextra                    2RHet                    
[11] 2LHet                     3LHet                    
[13] 3RHet                     U                        
[15] XHet                     
15 Levels: 2L 2LHet 2R 2RHet 3L 3LHet 3R 3RHet 4 U Uextra X XHet ... dmel_mitochondrion_genome
> unique(space(import.bed ('f.bed')))
 [1] chr2L                     2LHet                    
 [3] chr2R                     2RHet                    
 [5] chr3L                     3LHet                    
 [7] chr3R                     3RHet                    
 [9] chr4                      chrU                     
[11] Uextra                    chrX                     
[13] XHet                      YHet                     
[15] dmel_mitochondrion_genome
15 Levels: chr2L 2LHet chr2R 2RHet chr3L 3LHet chr3R 3RHet chr4 chrU ... dmel_mitochondrion_genome
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

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

other attached packages:
[1] rtracklayer_1.12.2 RCurl_1.5-0        bitops_1.0-4.1    

loaded via a namespace (and not attached):
[1] BSgenome_1.20.0     Biostrings_2.20.1   GenomicRanges_1.4.6
[4] IRanges_1.10.4      XML_3.4-0          
>


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