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.c...@googlemail.com wrote:
On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with
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?
You need to read the first four bytes of the file to see
On Tue, Jul 9, 2013 at 5:53 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
On Jul 8, 2013, at 3:33 PM, Peter Cock wrote:
The tools available in Galaxy are written in a range
of languages including C, Perl, R, etc. Yes, some are in Python,
but of those most are independent of Galaxy and can be
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.c...@googlemail.com wrote:
On Mon, Jul 8, 2013 at 10:24 PM,
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.c...@googlemail.com wrote:
On Mon, Jul 8, 2013 at 10:24 PM,
I will implement this if the galaxy team likes the approach.
We did this in ucsc genome browser code years ago: a single open_helper call
handles, gzip, http, ftp and pipes. No need to care about how the data is
compressed or where it data resides.
wouldn't it be great to be able to pipe
On Thu, Jul 4, 2013 at 9:49 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Dan,
Do these readers support gzip files?
reader = fastqVerboseErrorReader
reader = fastqReader
Presumably you are writing a Python script using this library?
The answer is a qualified yes.
On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
robert.baert...@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
On Mon, Jul 8, 2013 at 11:21 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
I respectfully disagree, If you want an extensible system, you should
always wrap primitive system level calls.
Any tools that opens a file that could be compressed would be affected.
That is a huge number of tools. Do
