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(a)googlemail.com> wrote:
> On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
> <robert.baertsch(a)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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