On 01/07/2013 12:32 PM, Nicolas Delhomme wrote:
Hi Martin, Marc,
I'm now implementing the use of BamFile objects in easyRNASeq and I like
them. I think it would be very useful if when constructing a BamFile the
existence of the path and index could be tested; i.e. this works:
BamFile("test.bam","test.bam.bai") although these files do not exist. Is
there a reason that this validation is not done? If there is, could a
validation parameter be added (set to FALSE by default to keep the current
behavior) that would check for the files' existence? The same goes for the
yieldSize argument, i.e. this works
BamFile("test.bam","test.bam.bai",yieldSize=-1), although I'm not sure what a
-1 yieldSize means. I can of course do these validations within easyRNASeq,
but anyone else building packages on top of BamFile would probably want to do
the same...
I want to be able to specify a BAM file without opening it, and then open it
later, e.g., in mclapply or after distributing to a cluster. Also, conceptually,
I want to distinguish between processing an entire BAM file -- provide me with
something for which isOpen(BamFile("foo")) == FALSE -- versus reading a chunk of
a BamFile, i.e., already open. So I separated BamFile creation from open().
I focus on open() in the above because opening the BAM file is a cheap way to
validate that the BAM file exists -- it could be local or remote (http or ftp,
so file.exists isn't sufficient) and even if the file 'exists' as Ryan mentions
it needs to actually be a BAM file so should, e.g., have a header. open() allows
for all of these possibilities. Also, the consequences of trying to open a
non-existent file results in a clear enough error
> open(BamFile("sdfs"))
Error in value[[3L]](cond) :
failed to open BamFile: file(s) do not exist:
'sdfs'
So against the votes of the other contributors to this thread, I haven't made a
change. Sorry about that.
I added a check that yieldSize is a non-negative scalar integer, or NA.
A related point unclear at the moment in the documentation is what the index
filename should be: i.e. scanBam expects as the index the same value as for
the bam filename (that assumes the user has not renamed his bam.bai file and
you never know what users might be doing... :-S ... ) but the BamFile Rd page
says:
file: A character vector of BAM file paths
> index: A character vector of indices (forBamFile);
so it's unclear to me what the index character vector should contain.
Tried to clarify that, it's just a character vector containing the path to the
index file. Generally, the code tries not to care about whether the index file
is specified with a '.bai' extension, or without.
Martin
Thanks again for this set of class, they're really handy!
Here's my sessionInfo:
R Under development (unstable) (2012-10-02 r60861) Platform:
x86_64-apple-darwin10.8.0 (64-bit)
locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages: [1] parallel stats graphics grDevices utils
datasets methods [8] base
other attached packages: [1] Rsamtools_1.11.14 Biostrings_2.27.8
GenomicRanges_1.11.21 [4] IRanges_1.17.24 BiocGenerics_0.5.6
BiocInstaller_1.9.6
loaded via a namespace (and not attached): [1] bitops_1.0-5 stats4_2.16.0
tools_2.16.0 zlibbioc_1.5.0
Cheers,
Nico
--------------------------------------------------------------- Nicolas
Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310 Email: nicolas.delho...@embl.de Meyerhofstrasse 1 -
Postfach 10.2209 69102 Heidelberg, Germany
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