[Bioc-sig-seq] skip the comment lines with read.BStringSet

[burak kutlu]

Hi
I am trying to fasta files into my session.
Is there a way to ignore the comment lines ( that start with #) when using read.BStringSet?
Here's the error I get when there are such lines at the beginning of the fasta file.

> read.BStringSet(file= 'burak.test', format = "fasta")
Error in .read.fasta.in.XStringSet(filepath, set.names, elementType, lkup) : 
  reading FASTA file     : ">" expected at beginning of line 1
> 

And this is how the file looks like
# Cwd: /home/pipeline
# Title: solid0131_20090316_1_H683_
>2_21_1117_F3
T00212313200111233020001110130100100
>2_21_1543_F3
T01022123123230121000121013333113111
.....

Many thanks
-burak



> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-unknown-linux-gnu 

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=C              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] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] ShortRead_1.4.0   lattice_0.17-26   BSgenome_1.14.2   Biostrings_2.14.8
[5] IRanges_1.4.9    

loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1   tools_2.10.1