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[Bioc-devel] BamFile validation

7 messages · Nicolas Delhomme, Henrik Bengtsson, Ryan +2 more

Original
Nicolas Delhomme
# 
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...


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.

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.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
Henrik Bengtsson
#
On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme <delhomme at embl.de> wrote:
Good idea - I propose argument 'mustExist'.

My $0.02

/Henrik
Nicolas Delhomme
# 
Just to clarify. I don't mean it needs to validate the BAM file (i.e. checking that it's properly formatted), so using file.exists on the provided file paths would be sufficient.

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 8 Jan 2013, at 02:47, Ryan Thompson wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Hi there,

FWIW system.file() has the 'mustWork' arg for this. Strange name though
since the man page suggests it only tests for existence, not that the
file can actually be open for reading.

H.

        
On 01/07/2013 11:11 PM, Nicolas Delhomme wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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On 01/07/2013 12:32 PM, Nicolas Delhomme wrote:

            

      
      
      
    

        
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.

            

      
      
      
    

        
> index:  A character vector of indices (forBamFile);

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Nicolas Delhomme
    

    

      
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Hi Martin,

        
On 8 Jan 2013, at 19:53, Martin Morgan wrote:

        

            

      
      
      
    

        
No need to. I hadn't thought of a use case as those you presented above where not checking makes perfect sense. I'll use open for validating.

            

      
      
      
    

        
Great thanks.

            

      
      
      
    

        
That was my perception :-) just wanted to be sure.

A related question, could you detail which functions require the bai index to  be present and which ones "just" benefit from it?

Cheers,

Nico