Load CLI result in Python?

[mikekestemont]

Thanks again for a great tool. Is there an easy way to load the result of an alignment created with the command line tool into a Python Collation object? (I want to use the Java tool for its speed, but keep the flexible visualization and postprocessing capabilities that I have in a Jupyter notebook.)

[rhdekker]

Hi. I am afraid there is no such possibility at the moment. The object that is visualised is actually the Variant Graph object, not the Collation object. The Collation object only holds the witness data, that is, the sequences of tokens to be aligned. The Variant Graph object contains the actual alignment. CollateX Java has an GraphML export that captures the alignment result in detail and writes it to disc. What is missing is a GraphML importer in CollateX Python that reads in the GraphML (which in itself is just an XML file) and recreates the Variant Graph object in memory, which then can be visualised in whatever way is desired.