Graphml via Networkx compatibility question

HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd

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Graphml via Networkx compatibility question #153

Closed markb729 closed 5 years ago

markb729 commented 5 years ago

Based on Networkx v1.9.1, graphs created and exported by HINGE have good compatibility with other software such as Gephi. However, others like iGraph [fail] and yEd [poor rendering] do not. From your experience with Networkx, do you have any information regarding issues like namespaces used in HINGE, for example http://graphml.graphdrawing.org/specification.html that could be causing these incompatibilities?

markb729 commented 5 years ago

I've come up with a solution that at least allows iGraph to import and plot graphml files rendered by Networkx v1.9.1 in HINGE. The offending issue was a lack of an explicit XML declaration. At least this was simple enough.

<?xml version="1.0" encoding="UTF-8" standalone="no"?>