[BioC] Small bug in function 'countskip.FASTA.entries' from package 'altcdfenvs'

[Norman Pavelka]

Dear Laurent Gautier,

First of all, let me express my gratitudine and compliments for the 
very important package you contributed and I apologize for this long 
message (that I am CCing to the BioC list).

I'm currently using 'altcdfenvs' to re-map probe sequences from Affy 
MOE430 2.0 arrays and I noticed a small but reproducible bug in the 
function 'countskip.FASTA.entries'.

When I follow the vignette step-by-step, no errors show up in my 
session:

library(altcdfenvs)
fasta.filename <- "Mus_musculus.NCBIM34.nov.cdna.fa"
con <- file(fasta.filename, open = "r")
n <- countskip.FASTA.entries(con)
close(con)
cat(n,"entries read\n")

Of course, I can cut and paste the same chunk of code into a brand new 
R function and save the file:

test.countskip.FASTA.entries <- function(fasta.filename) {
	library(altcdfenvs)
	con <- file(fasta.filename, open = "r")
	n <- countskip.FASTA.entries(con)
	close(con)
	cat(n,"entries read\n")
}

And, of course, I can source the function from the new file and again I 
have no errors, if I run:
test.countskip.FASTA.entries("Mus_musculus.NCBIM34.nov.cdna.fa")

But _magically_, if I close the R session, reload R and source the file 
containing my function, I get the following error:

 > test.countskip.FASTA.entries("Mus_musculus.NCBIM34.nov.cdna.fa")
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

         Vignettes contain introductory material.
         To view, simply type 'openVignette()' or start with 
'help(Biobase)'.
         For details on reading vignettes, see the openVignette help 
page.

Loading required package: affy
Loading required package: matchprobes
Loading required package: makecdfenv
Error in readLines(con, n = 1) : object "con" not found

Why?

When I inspected the source of function 'countskip.FASTA.entries', I 
noticed that the argument defining the connection to the file 
containing the FASTA entries was missing. The function was therefore 
using the 'con' object found in the global environment, rather than the 
one passed as an argument. But when R was reloaded, the 'con' object 
disappeared and the error showed up. In other words, the vignette code 
chunk worked fine for me just by chance! ;-)

I thus changed the function in the following way:

### My personal modification of function 'countskip.FASTA.entries'
### to allow a file connection to be passed to the function
my.countskip.FASTA.entries <- function (con, linebreaks = 3000) {
	i <- as.integer(0)
	fs <- read.FASTA.entry(con)
	while (!identical(fs$header, character(0)) && !identical(fs$sequence, 
NULL)) {
		i <- i + 1
		fs <- read.FASTA.entry(con)
		}
	return(i)
	}
### End of my modified function

When I now modify my test function to use 'my.countskip.FASTA.entries' 
instead of 'countskip.FASTA.entries', I have no errors regardless 
whether I'm working in a fresh or older R session... In addition, now 
I'm allowed to have more than one file connection around and specify 
the one I would like to pass to 'my.countskip.FASTA.entries'...

BTW, what is the argument 'linebreaks' good for? It seems not to be 
used inside the function...

Hope this feed-back was worth reporting!

Thank you again and best wishes,
Norman

 > sessionInfo()
R version 2.2.0, 2005-10-06, powerpc-apple-darwin7.9.0

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

other attached packages:
  altcdfenvs  makecdfenv matchprobes        affy     Biobase
     "1.4.0"     "1.8.0"     "1.2.1"     "1.8.1"     "1.8.0"

Norman Pavelka
Department of Biotechnology and Bioscience
University of Milano-Bicocca
Piazza della Scienza, 2
20126 Milan, Italy

Phone: +39 02 6448 3556
Fax: +39 02 6448 3552