Pipeline

Pipeline for VarGenPath

vargenpath.pipeline.get_vargenpath_network(*, variant_list, network_name='VarGenPath network', linkset_path='/home/docs/checkouts/readthedocs.org/user_builds/vargenpath/checkouts/latest/data/wikipathways-20190610-hsa.xgmml', session_path=None, image_path=None, extend_network=True, image_type='svg', network_path=None, network_file_path='cyjs')[source]

Pipeline for creating vargenpath network.

Parameters

  • network_file_path (Optional[str]) – the type of network file to be saved.

  • network_path (Optional[str]) – if input path, the cytoscape network will be saved to this path.

  • variant_list (list) – list of variants.

  • network_name (Optional[str]) – the name of the network.

  • linkset_path (Optional[str]) – the path to the linkset to extend network.

  • session_path (Optional[str]) – if input path, the cytoscape session will be saved to this path.

  • image_path (Optional[str]) – if input path, the image of the network will be saved to this path.

  • extend_network (bool) – if true, the network will be extended.

  • image_type (Optional[str]) – the type of the image to be saved.

Return type

dict

Returns

cytoscape network