Utilities

Utilities for VarGenPath.

vargenpath.utils.extend_vargen_network(linkset_path, client)[source]

Extend network with linkset in xgmml format. CytargetLinker provide a number of linksets that can be downloaded and used. https://cytargetlinker.github.io/pages/linksets

Parameters

  • client (CyRestClient) – cystoscape client.

  • linkset_path (str) – the path to the linkset used to extended the network.

Return type

dict

Returns

vargenpath.utils.file_reader(file)[source]

Read text file.

Parameters

file (File) – text file containing the variants.

Return type

list

Returns

a list of variants.

vargenpath.utils.get_associated_genes(variants_list)[source]

Get variant gene information from BioMart. More information on BioMart here: https://www.ensembl.org/info/data/biomart/index.html

Parameters

variants_list (list) – the list with variant ids.

Return type

DataFrame

Returns

dataframe with variant and gene information

vargenpath.utils.get_cytoscape_connection()[source]

Connect to cytoscape.

Return type

CyRestClient

vargenpath.utils.save_image(*, network_image, image_type='SVG (*.svg)')[source]

Save network image. Types that can be used are JPEG (.jpeg, *.jpg), PDF (.pdf), PNG (.png), PostScript (.ps), SVG (*.svg)

Parameters

  • network_image (str) – path to save the network image.

  • image_type (str) – type of image to be saved.

Return type

str

Returns

vargenpath.utils.save_network(*, network_path, file_type)[source]

Save network file.

Parameters

  • network_path – path to save the network file.

  • file_type – type of file to be saved.

Return type

str

Returns

vargenpath.utils.save_session(*, session_file, client)[source]

Save cystoscape session.

Parameters

  • session_file (str) – path to save the session.

  • client (CyRestClient) – cystoscape client.

Return type

str

Returns

vargenpath.utils.var_genes_network(*, variants_genes_df, network_name='VarGenPath network', client)[source]

Create cytoscape network from dataframe.

Parameters

  • variants_genes_df (DataFrame) – dataframe containing the vaiants, genes and their interaction

  • network_name (str) – the name of the network.

  • client – the cystocape client.

Return type

dict

Returns

cytoscape network