[BioC] cosmo for particular sequences

[Ana Richardson [guest]]

Hi! I'm trying to find motifs in a file of 50 sequences in FASTA format, they are particular in that they have no "G" so when I run this:
>library(cosmo)
> seqal <- system.file("Exfiles/short702k.FASTA", package="cosmo")
> res <- cosmo(seqs=seqal, constraints="None", minW=10, maxW=10, models="TCM")

I get the message:
new Irange 202 is greater than pre-calculated Irange 0. numSites = 2. Exiting.

If I add only one ficticious G in one of the sequences then it works, but I get some G's in the seqlogo plot

Ana 


 -- output of sessionInfo(): 

new Irange 202 is greater than pre-calculated Irange 0. numSites = 2. Exiting.

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