biostrings: handling genomic information as strings
===================================================

The module reflects the content of the R/Bioconductor
package *Biostrings*. It defines Python-level classes
for the R/S4 classes, and gives otherwise access to
R-level commands the usual :mod:`rpy2:robjects` way.

The variable  :data:`biostrings_env` in the module
is an :class:`rpy2.robjects.REnvironment` for the
modules namespace. Accessing explicitly a module's
object is then straightforward. Example:

>>> biostrings.biostrings_env['RNA_ALPHABET']


The class inheritance diagram is useful for having
an overview of how (biological) strings
are modelled.

.. inheritance-diagram:: bioc.biostrings
   :parts: 1

.. automodule:: bioc.biostrings
   :members:
   :undoc-members:


bsgenome: strings information for a complete genome
===================================================

Examples
--------


>>> import bioc.bsgenome
>>> genomes = bioc.bsgenome.__rpackage__.available_genomes()
>>> tuple(genomes)
('BSgenome.Amellifera.BeeBase.assembly4',
 'BSgenome.Amellifera.UCSC.apiMel2',
 'BSgenome.Athaliana.TAIR.01222004',
 'BSgenome.Athaliana.TAIR.04232008',
 'BSgenome.Btaurus.UCSC.bosTau3',
 'BSgenome.Btaurus.UCSC.bosTau4',
 'BSgenome.Celegans.UCSC.ce2',
 'BSgenome.Cfamiliaris.UCSC.canFam2',
 'BSgenome.Dmelanogaster.UCSC.dm2',
 'BSgenome.Dmelanogaster.UCSC.dm3',
 'BSgenome.Drerio.UCSC.danRer5',
 'BSgenome.Ecoli.NCBI.20080805',
 'BSgenome.Ggallus.UCSC.galGal3',
 'BSgenome.Hsapiens.UCSC.hg17',
 'BSgenome.Hsapiens.UCSC.hg18',
 'BSgenome.Hsapiens.UCSC.hg19',
 'BSgenome.Mmusculus.UCSC.mm8',
 'BSgenome.Mmusculus.UCSC.mm9',
 'BSgenome.Ptroglodytes.UCSC.panTro2',
 'BSgenome.Rnorvegicus.UCSC.rn4',
 'BSgenome.Scerevisiae.UCSC.sacCer1',
 'BSgenome.Scerevisiae.UCSC.sacCer2')

The genome names can be passed to biocLite (see the introduction) for
an automagic download and install of the corresponding genome package.

>>> tuple(bioc.bsgenome.__rpackage__.installed_genomes())
('BSgenome.Celegans.UCSC.ce2',
 'BSgenome.Hsapiens.UCSC.hg18',
 'BSgenome.Hsapiens.UCSC.hg19')

Installed genomes can be imported, since they are R packages.

>>> from rpy2.robjects.packages import importr
>>> ce2_genome = importr('BSgenome.Celegans.UCSC.ce2')


>>> ce2_genome.Celegans
<BSgenome - Python:0x2a80058 / R:0x4cbdf10>
>>> print(ce2_genome.Celegans.seqlengths)
    chrI    chrII   chrIII    chrIV     chrV     chrX     chrM 
15080483 15279308 13783313 17493791 20922231 17718849    13794 
>>> ce2_genome.Celegans['chrI']
<DNAString - Python:0x2a80878 / R:0x53ac7e4>


Docstrings
----------


The class inheritance diagram is useful for having
an overview of how the representation of genomes
is organized.

.. inheritance-diagram:: bioc.bsgenome
   :parts: 2

.. automodule:: bioc.bsgenome
   :members:
   :undoc-members: