Case study: Analysis of the C. elegans genome
=============================================


Example with *C. elegans*:

.. literalinclude:: example_celegans.py
   :start-after: #-- setup
   :end-before: #-- download repeats from Sanger

Listing the sequence names:

>>> tuple(celegans.seqnames)
['chrI', 'chrII', 'chrIII', 'chrIV', 'chrV', 'chrX', 'chrM']


Extracting a chromosome sequence is working the same way
as it would with R:

>>> chrI = celegans['chrI']
>>> chrI
<DNAString - Python:0x9ca44ac / R:0xbc1a8c0>


.. literalinclude:: example_celegans.py
   :start-after: #-- download repeats from Sanger
   :end-before: #-- match repeats


For speed, we only consider a subset of the sequences for now.

.. literalinclude:: example_celegans.py
   :start-after: #-- subset of the repeated sequences
   :end-before: #-- match repeats



.. literalinclude:: example_celegans.py
   :start-after: #-- match repeats
   :end-before: #-- information about the matches



.. literalinclude:: example_celegans.py
   :start-after: #-- information about the matches
   :end-before: #-- data.frame with the results