great. Let's put the bx-python calls in a galaxy_open helper function. On Jul 8, 2013, at 3:20 PM, James Taylor wrote:
open_compressed in bx-python does this already (for bz2 as well).
On Jul 8, 2013, at 5:58 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch <robert.baertsch@gmail.com> wrote:
Peter and Dan, I like the idea of replacing all open() with galaxy_open() in all tools. You can tell the format by looking at the first 4 byes (see C code below from the UCSC browser team). Is there some pythonic way of overriding open?
There is monkey patching (replace the current 'open' function with your modified version), but that is not a good idea in general.
In any case, this would only affect the small number of Python tools which happen to use the Galaxy parsing libraries - which is a very small fraction of the tools in Galaxy. Most of the tools in Galaxy are compiled programs and are entirely separate.
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