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1 parent 89d55d0 commit 062816ba4114e922bec801b68ca5471538dec27f @daler committed Mar 6, 2012
Showing with 16 additions and 16 deletions.
  1. +8 −7 README.rst
  2. +0 −4 docs/source/index.rst
  3. +1 −1 docs/source/topical-iterators.rst
  4. +7 −4 docs/source/topical-wrapping.rst
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15 README.rst
@@ -5,24 +5,25 @@ Overview
Python. See full online documentation, including installation instructions, at
http://packages.python.org/pybedtools/.
-Created by Ryan Dale 2010. Copyright 2010, 2011, 2012 Ryan Dale, all rights
-reserved.
+*Created by Ryan Dale 2010*
+
+*Copyright 2010, 2011, 2012 Ryan Dale, all rights
+reserved.*
`pybedtools` is released under the GPLv2 license; see LICENSE.txt for more
info.
.. note::
- If you use :mod:`pybedtools` in your work, please cite the
- `pybedtools manuscript <http://bioinformatics.oxfordjournals.org/content/27/24/3423>`_:
+ If you use :mod:`pybedtools` in your work, please cite the `pybedtools
+ manuscript <http://bioinformatics.oxfordjournals.org/content/27/24/3423>`_
+ and the `BEDTools manuscript
+ <http://bioinformatics.oxfordjournals.org/content/26/6/841.short>`_:
Dale RK, Pedersen BS, and Quinlan AR. 2011. *Pybedtools: a flexible
Python library for manipulating genomic datasets and annotations*.
Bioinformatics 27(24):3423-3424.
- And the `BEDTools manuscript
- <http://bioinformatics.oxfordjournals.org/content/26/6/841.short>`_:
-
Quinlan AR and Hall IM, 2010. *BEDTools: a flexible suite of utilities
for comparing genomic features*. Bioinformatics 26(6):841–842.
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4 docs/source/index.rst
@@ -5,8 +5,6 @@
.. include:: includeme.rst
-.. _PDF version: pybedtools_manual.pdf
-
Welcome to pybedtools's documentation!
======================================
@@ -26,8 +24,6 @@ like to cover:
* Finally, doctested module documentation can be found in :ref:`autodoc`.
-A `PDF version`_ of this manual is also available.
-
Contents:
---------
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2 docs/source/topical-iterators.rst
@@ -11,7 +11,7 @@ objects also have the ability to "stream", much like piping in Unix. That
is, the data are created only one line at a time in memory, instead of
either creating a list of all data in memory or writing all data to disk.
-.. warning::
+.. note::
You'll need to be careful when using :mod:`BedTool` objects as
generators, since any operation that reads all the features of a
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11 docs/source/topical-wrapping.rst
@@ -37,13 +37,16 @@ effectively be ignored.
Add the :func:`_wraps` decorator
--------------------------------
-This is where most of the work happens.
+This is where most of the work happens.
Since most of the work of wrapping BEDTools programs needs to happen every
time a new program is wrapped, this work is abstracted out into the
-:func:`_wraps` function. The :func:`_wraps` docstring and source is the
-best place to learn the details on what it's doing; here we'll focus on
-using it.
+:func:`_wraps` function.
+
+.. note::
+
+ The :func:`_wraps` docstring and source is the best place to learn the
+ details on what it's doing; here we'll focus on using it.
Our hypothetical program, `newProgramBed`, takes `-a` as the first input.
We'd like to have `-a` implicitly be passed as whatever our

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