[bip] Playing with pygr and yeast

[Humberto Ortiz-Zuazaga]

Titus Brown wrote:
> On Fri, Dec 07, 2007 at 06:10:26AM -0400, Humberto Ortiz-Zuazaga wrote:
> -> Titus Brown wrote:
> -> > Hi all,
> -> > 
> -> > I wrote up a document on how to use pygr to put annotations on the yeast
> -> > genome and then query those annotations by position:
> -> > 
> -> > http://iorich.caltech.edu/~t/bio+python/pygr/annotating-yeast.html
> -> > 
> -> 
> -> Titus, thank you very much. That is exactly the information I need to
> -> start some projects here at the UPR. I'll follow through the tutorial,
> -> and if I hit some rough spots I'll send you mail.
> 
> Great, that's what I want to hear!
> 
> Note that the entire document is a doctest, and you can use darcs to
> grab it:
> 
> 	darcs get http://iorich.caltech.edu/~t/bio+python/
> 
> So if you can't get the code examples to work, I'll eat my hat (or ask
> the authors of pygr eat it for me ;)
> 
> cheers,
> --titus

I just worked out the example with hg18 and ensGene.txt.gz, it worked
smoothly.

One hiccup is that svn motility wouldn't build on an x86_64 machine
running Centos 5. I had to pass CXXFLAGS to cmake:

cmake -DCMAKE_CXX_FLAGS="-fPIC" .

Otherwise, it compiles motility but can't link the .so.

I also suggest wrapping the last example, in case they use a motif that
has more than one overlap:

>>> for overlap in overlaps:
...     overlapping = overlap.keys()
...     for upstream_annot in overlapping:
...         print upstream_annot.gene_name

Thanks again for the example and the tutorials. I'm so happy, I won't
even hold you to your promise to eat your hat. :-)

-- 
Humberto Ortiz-Zuazaga
Programmer-Archaeologist
University of Puerto Rico
http://www.hpcf.upr.edu/~humberto/

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