mako io

The io module can be used to write network files to a Neo4j database according to mako’s database schema. Networks can be imported as graphml files, gml files or as weighted edge lists (text files with three columns: source nodes, target nodes and the edge weights). The -fp prefix contains the shared file path, so there is no need to write the full file path, partial file paths or just filenames are sufficient if -fp is used.

The io module also has options for adding extra metadata to the Neo4j database. If a tab-delimited edge list is supplied with existing nodes in the 1st column and new properties in the 2nd column, this is used to create a new Property node with relationships containing property values.If all property values are strings, a new node is made with a label identical to the column value and the node name as the string value.

Finally, the module can delete and export networks or derived sets (generated with the netstats module) to a running instance of Cytoscape or to a graphml file. To run these operations, the -net parameter should be given names of Network or Set names in the Neo4j database.

• -net One or more (filepaths of) network files, or Network / Set names
• -del Name(s) of Network or Set node(s) that should be deleted
• -fasta Name(s) of FASTA files, e.g. GreenGenes FASTA files
• -cyto If flagged, exports networks listed in -net to Cytoscape
• -meta One or more tab-delimited files with node metadata (as a 2-column table). Column names are used to match node labels
• -w If flagged, writes networks listed in -net to graphml