pybedtools version 0.6.2

[Ryan Dale]

Hi all,

On the heels of BEDTools 2.17 release, I've just released the
corresponding pybedtools v0.6.2.

pybedtools v0.6.2 wraps the tools new in BEDTools 2.17, and adds lots of
bugfixes and features of its own.

The complete documentation is at http://packages.python.org/pybedtools/,
and the specific changes and new features in this version are listed at
http://packages.python.org/pybedtools/changes.html#changes-in-v0-6-2.

As always, comments, suggestions, and bug reports are all welcome.

-ryan

[Urban, John]

Hi Ryan,

Is there a pdf version of the complete documentation for pybedtools v0.6.2?  If so please let me know where to find it.

Best,

  John

--
John Urban

Ph.D. Candidate

NSF Graduate Research Fellow

Brown University

Dept. of Molecular Biology, Cell Biology, and Biochemistry

Laboratory of Susan Gerbi, Sydney Frank Hall 257

Providence, RI 02906

john_...@brown.edu

[Ryan Dale]

Hi John -

The docs are written in sphinx (http://sphinx-doc.org/), so technically they can be built as latex, PDF, epub, etc.  However when I just tried to do this there were a lot of pdflatex errors (I suspect because of docstring formatting, perhaps in both pybedtools as well as bedtools proper).  I'll need to debug this further.

In the meantime, you can always get the source from github, change to the docs subdirectory, and build the docs yourself like this:

git clone git://github.com/daler/pybedtools.git
cd pybedtools/docs
make html

then open pybedtools/docs/build/html/index.html for you offline copy.

There are other flavors available too, just run make with no argument to see the options.

-ryan

[Urban, John]

Hi Ryan,

Thanks for your quick and detailed response. I tried exactly what you said:

     git clone git://github.com/daler/pybedtools.git
     cd pybedtools/docs
     make html

But received this message:

sphinx-build -b html -d build/doctrees   source build/html

make: sphinx-build: No such file or directory

make: *** [html] Error 1

I ran make without arguments to see the other flavors, then tried 'make latexpdf' and received:

sphinx-build -b latex -d build/doctrees   source /tmp/doc-pybedtools/latex

make: sphinx-build: No such file or directory

make: *** [latexpdf] Error 1

Assuming this was because I did not have sphinx, I did:

pip install sphinx

Then I ran 'make html' and received:

sphinx-build -b html -d build/doctrees   source build/html

Making output directory...

Running Sphinx v1.1.3

Exception occurred:

  File "/Users/johnurban/Desktop/pybedtools/pybedtools/__init__.py", line 9, in <module>

    from cbedtools import Interval, IntervalFile, overlap, \

ImportError: No module named cbedtools

The full traceback has been saved in /var/folders/n1/37wvt0y95bx5b4hnp6r7hs4h0000gn/T/sphinx-err-aaJElt.log, if you want to report the issue to the developers.

Please also report this if it was a user error, so that a better error message can be provided next time.

Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>,

or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!

make: *** [html] Error 1

There is pybedtools/docs/build/html, but it is empty.

Any ideas I should try?

It may or may not be relevant that I put pybedtools on my MacBook Pro previously by 'pip install pybedtools'.

Best,

  John

[ryan]

Hi John - 

In the newly-checked-out pybedtools dir, try running this:

python setup.py build_ext -i

This will Cython-ize some of the source code (without actually installing pybedtools a second time), hopefully getting you the file that sphinx was complaining about.  You'll need to have Cython installed, though.

Then compile the docs again:

cd docs

make html

Does that work?

-ryan

[Urban, John]

Hi Ryan, 

That did the trick. Thanks for helping out and sharing some of your expertise (and for pybedtools)!

Best,

  John