Welcome to PyOpenWorm’s documentation!¶
Contents:
Modules¶
PyOpenWorm¶
OpenWorm Unified Data Abstract Layer.
Classes¶
- class PyOpenWorm.Network¶
- aneuron(name)¶
Get a neuron by name
Parameters: name – Name of a c. elegans neuron Returns: Corresponding neuron to the name given Return type: PyOpenWorm.Neuron
- as_networkx()¶
Get the network represented as a NetworkX graph
Nodes include neuron name and neuron type. Edges include kind of synapse and neurotransmitter.
Returns: directed graphs with neurons as verticies and gap junctions and chemical synapses as edges Return type: NetworkX.DiGraph
- neurons()¶
Get all neurons by name
Returns: A list of all neuron names Return type: list
- class PyOpenWorm.Neuron(name)¶
- GJ_degree()¶
Get the degree of this neuron for gap junction edges only
Returns: total number of incoming and outgoing gap junctions Return type: int
- Syn_degree()¶
Get the degree of a this neuron for chemical synapse edges only
Returns: total number of incoming and outgoing chemical synapses Return type: int
- get_reference(type, item='')¶
Get a reference back that provides the evidence that this neuron is associated with the item requested as a list of URLs.
Example:
>>>ader = PyOpenWorm.Neuron('ADER') >>>ader.receptors() ['ACR-16', 'TYRA-3', 'DOP-2', 'EXP-1'] #look up what reference says this neuron has a receptor EXP-1 >>>ader.get_reference(0,'EXP-1') ['http://dx.doi.org/10.100.123/natneuro'] #look up what reference says this neuron has a neighbor DD5 >>>ader.get_reference(1, 'DD5') ['http://dx.doi.org/20.140.521/ploscompbiol']
Parameters: - type – The kind of thing to search for. Valid options are: 0=receptor, 1=neighbor
- item – Name of the item requested, if appropriate
Returns: a list of URLs that points to references
Return type: list
- name()¶
Get name of this neuron (e.g. AVAL)
Returns: the name Return type: str
- receptors()¶
Get receptors associated with this neuron
Returns: a list of all known receptors Return type: list
- type()¶
Get type of this neuron (motor, interneuron, sensory)
Returns: the type Return type: str
- type_networkX()¶
Get type of this neuron (motor, interneuron, sensory)
Use the networkX representation as the source
Returns: the type Return type: str
- type_semantic()¶
Get type of this neuron (motor, interneuron, sensory)
Use the semantic database as the source
Returns: the type Return type: str
- class PyOpenWorm.Worm¶
- get_neuron_network()¶
Get the network object
Returns: An object to work with the network of the worm Return type: PyOpenWorm.Network
- get_semantic_net()¶
- Get the underlying semantic network as an RDFLib Graph
Returns: A semantic network containing information about the worm Return type: rdflib.ConjunctiveGraph
- muscles()¶
Get all muscles by name
Returns: A list of all muscle names Return type: list