[BioC] rtracklayer mystery with ucscTableQuery

[Sigal Blay]

library(rtracklayer)
genes <- c("uc003wgi.1", "uc010lpn.2", "uc010lpm.1")
session <- browserSession()


# Search only for the first gene - failed with a warning message
> query1 <- ucscTableQuery(session, "knownGene", table="kgXref", names=genes[1])
> t1 <- getTable(query1)
Warning message:
In read.table(f, sep = "\t", header = TRUE) :
  incomplete final line found by readTableHeader on ''

# If I don't specify the genes, the first one is found
> query2   <- ucscTableQuery(session, "knownGene", table="kgXref")
> t2<-getTable(query2)

> t2[t2[,"kgID"]==genes[1],]	# 1st gene found
> t2[t2[,"kgID"]==genes[2],]	# 2nd gene not found
> t2[t2[,"kgID"]==genes[3],]	# 3rd gene not found

# if I specify the genes, first and second are found, but not the third
> query3   <- ucscTableQuery(session, "knownGene", table="kgXref", names = genes)
> t3 <- getTable(query3)

> t3[t3[,"kgID"]==genes[1],]	# 1st gene found
> t3[t3[,"kgID"]==genes[2],]	# 2nd gene found
> t3[t3[,"kgID"]==genes[3],]	# 3rd gene not found



> sessionInfo()
R version 2.10.1 (2009-12-14) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

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

other attached packages:
[1] rtracklayer_1.6.0 RCurl_1.3-1       bitops_1.0-4.1   

loaded via a namespace (and not attached):
[1] Biobase_2.6.1      Biostrings_2.14.12 BSgenome_1.14.2    IRanges_1.4.14    
[5] XML_2.6-0