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[Bioc-devel] Bioc-devel Digest, Vol 152, Issue 10

2 messages · rcaloger, Dario Strbenac

Original
rcaloger
# 
Hi Dario,
I am the maintainer of chimera package
thank for the info I am going to check which is the problem in 
importFusionData.
There is only one example of data import, because of limits in package size.
An other example can be retrieved from:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", 
"Chimeric.out.junction.zip", mode="wb")

I check the example:
tmp <- importFusionData("fusionmap", 
paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", 
sep=""), org="hg19")
and it seems to import correctly the fusionmap data.

Same  happens with:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", 
"Chimeric.out.junction.zip", mode="wb")
unzip("Chimeric.out.junction.zip")
tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", 
min.support=100)

Could please send me the code you have run and could you please describe 
the issue you encountered?
Cheers
Raf

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      Dario Strbenac
    

    

      
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Good day,

The problem is simply caused by an incorrectly typed file path. The error message isn't clear about this and describes some temporary file name (based on today's date and time) which is confusing. Perhaps the importFusionData function could be made more robust by checking for the file's existence at the beginning of the function. For example,

if(file.exists(filename))
    # Do fusion file import.
else
    stop("Could not find the specified fusion file.")

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia