[Biopython-dev] test for affy.CelFile

[Vincent Davis]

>
> I don't know enough about CEL files to answer this, but is there no easy
> way to take a subsample of the file? Even zipped this is quite big.
>

​Yes, for CEL V3 it is easy and I have found a program that will convert
between V3 and V4 so I should be able to make a V4 that has the same data.
I do have a different V4 file also.

CelFile.py has no error handling or for that matter any verification that
the file handel is a CEL file. I think at this time it can be passed any
file handle with no error. I plan to first add checks for CEL file version,
verify number of columns and number of rows are correct, maybe other simple
checks. With that in mind I figured I would use "real" CEL files for
testing locally then make a sample file for distribution.

Would the bz2.open() method not be simpler? Or gzip.open() should
> work if you switch the compression.


​Yes, I did not know about this.


Vincent Davis
720-301-3003