hi,

i'm trying to extract the UCSC sequence levels for Canis familiaris using the function extractSeqlevelsByGroup() from the GenomeInfoDb package, but I stumbled onto the following error:

library(GenomeInfoDb)
library(BSgenome.Cfamiliaris.UCSC.canFam3)

extractSeqlevelsByGroup(species=organism(Cfamiliaris), style="UCSC", group="auto")
Error in extractSeqlevelsByGroup(species = organism(Cfamiliaris), style = "UCSC",  :
  The style specified by 'UCSC' does not have a compatible entry for the species Canis lupus familiaris

while the analogous call works perfectly for Homo sapiens:

library(BSgenome.Hsapiens.UCSC.hg38)
extractSeqlevelsByGroup(species=organism(Hsapiens), style="UCSC", group="auto")
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"
 [8] "chr8"  "chr9"  "chr10" "chr11" "chr12" "chr13" "chr14"
[15] "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21"
[22] "chr22"

i guess something is wrong with the mapping from the out of organism to the GenomeInfoDb data file at GenomeInfoDb/inst/extdata/dataFiles, see:

organism(Cfamiliaris)
[1] "Canis lupus familiaris"
organism(Hsapiens)
[1] "Homo sapiens"

thanks for your help, session information below.

robert.
ps: sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)

locale:
 [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8    
 [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8   
 [7] LC_PAPER=en_US.UTF8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.1      
 [2] BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0
 [3] BSgenome_1.38.0                        
 [4] rtracklayer_1.30.1                     
 [5] Biostrings_2.38.0                      
 [6] XVector_0.10.0                         
 [7] GenomicRanges_1.22.0                   
 [8] GenomeInfoDb_1.6.0                     
 [9] IRanges_2.4.1                          
[10] S4Vectors_0.8.0                        
[11] BiocGenerics_0.16.0                    
[12] vimcom_1.2-3                           
[13] setwidth_1.0-4                         
[14] colorout_1.1-0                         

loaded via a namespace (and not attached):
 [1] zlibbioc_1.16.0            GenomicAlignments_1.6.1   
 [3] BiocParallel_1.4.0         tools_3.2.2               
 [5] SummarizedExperiment_1.0.0 Biobase_2.30.0            
 [7] lambda.r_1.1.7             futile.logger_1.4.1       
 [9] futile.options_1.0.0       bitops_1.0-6              
[11] RCurl_1.95-4.7             Rsamtools_1.22.0          
[13] XML_3.98-1.3              

Hi Robert,

Even though there is an entry for Canis_familiaris in the genome style db included in GenomeInfoDb:

names(genomeStyles())
#  [1] "Arabidopsis_thaliana"     "Caenorhabditis_elegans"  
#  [3] "Canis_familiaris"         "Cyanidioschyzon_merolae" 
#  [5] "Drosophila_melanogaster"  "Homo_sapiens"            
#  [7] "Mus_musculus"             "Oryza_sativa"            
#  [9] "Populus_trichocarpa"      "Rattus_norvegicus"       
# [11] "Saccharomyces_cerevisiae" "Zea_mays"             

the failure you got with

extractSeqlevelsByGroup(organism(Cfamiliaris), style="UCSC", group="auto")

is because the supplied organism (organism(Cfamiliaris)) is "Canis lupus familiaris" and extractSeqlevelsByGroup() didn't know how to map it to Canis_familiaris. Thanks for catching this!

I just committed the following change to GenomeInfoDb, which addresses the problem:

hpages@latitude:~/svn/bioconductor/Rpacks_3_2/GenomeInfoDb$ svn log -r 110226
------------------------------------------------------------------------
r110226 | hpages@fhcrc.org | 2015-11-02 14:51:50 -0800 (Mon, 02 Nov 2015) | 12 lines

Mapping from user-supplied species/organism to officially supported organism
(as returned by 'names(genomeStyles())') now ignores the 2nd part (e.g. "lupus"
in "Canis_lupus_familiaris"). With this change, things like

  extractSeqlevelsByGroup("Canis lupus familiaris", style="UCSC", group="auto")

now work even though only "Canis_familiaris" is officially supported.
...

This is in GenomeInfoDb 1.6.1 (and GenomeInfoDb 1.7.3 in BioC devel) which should become available tomorrow via biocLite().

Cheers,

H.