bbcflib::genrep::GenRep Class Reference

List of all members.

Public Member Functions
def	__init__
def	assembly
def	is_up
def	assemblies_available
def	get_sequence
def	get_genrep_objects
Public Attributes
	url
	root

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Detailed Description

Attributes:

.. attribute:: url

    GenRep url ('genrep.epfl.ch').

.. attribute:: root

    Path to GenRep indexes.

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Member Function Documentation

def bbcflib::genrep::GenRep::__init__	(		self,
			url = None,
			root = None,
			config = None,
			section = 'genrep'
	)

Create an object to query a GenRep repository.

GenRep is the in-house repository for sequence assemblies for the
BBCF in Lausanne.  This is an object that wraps its use in Python
in an idiomatic way.

Create a GenRep object with the base URL to the GenRep system, and
the root path of GenRep's files.  For instance::

    g = GenRep('genrep.epfl.ch', '/path/to/genrep/indices')

To get an assembly from the repository, call the assembly
method with either the integer assembly ID or the string assembly
name.  This returns an Assembly object::

    a = g.assembly(3)
    b = g.assembly('mm9')

You can also pass this to the Assembly call directly::

    a = Assembly(assembly='mm9',genrep=g)

def bbcflib::genrep::GenRep::assemblies_available	(		self,
			assembly = None
	)

Return a list of assemblies available on genrep, or tells if an
assembly with name *assembly* is available.

def bbcflib::genrep::GenRep::assembly	(		self,
			assembly,
			intype = 0
	)

Backward compatibility

def bbcflib::genrep::GenRep::get_genrep_objects	(		self,
			url_tag,
			info_tag,
			filters = None,
			params = None
	)

Get a list of GenRep objets.

:param url_tag: the GenrepObject type (plural)
:param info_tag: the GenrepObject type (singular)
:param filters: a dict that is used to filter the response
:param params: to add some parameters to the query from GenRep.

Example:

To get the genomes related to 'Mycobacterium leprae' species::

    species = get_genrep_objects('organisms', 'organism', {'species':'Mycobacterium leprae'})[0]
    genomes = get_genrep_objects('genomes', 'genome', {'organism_id':species.id})

def bbcflib::genrep::GenRep::get_sequence	(		self,
			chr_id,
			coord_list,
			path_to_ref = None
	)

Parse a slice request to the repository.

:param chr_id: (int) chromosome number (keys of Assembly.chromosomes).
:param coord_list: (list of (int,int)) sequences' (start,end) coordinates.
:param path_to_ref: (str) path to a fasta file containing the whole reference sequence.

def bbcflib::genrep::GenRep::is_up

(

self

)

Check if genrep webservice is available

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The documentation for this class was generated from the following file:

• /home/rougemon/Data/pipelines/libv2/bbcflib/bbcflib/genrep.py