Best way to find neighbors of a node in a VG graph?
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2.2 years ago
samantha.hao ▴ 10

Hi,

What is the best way to extract the neighboring nodes of a given node ID in a VG graph? I can think of a couple, but it's not clear which would be the most direct way:

  1. vg find -n ID -c 1 -x graph.xg | vg view -j - would give a json that contains the node IDs.

  2. vg stats -S graph.vg would output a table where I could search for the desired node ID lines.

There are a few more methods I can think of that indirectly give me the information by parsing a JSON, but I was wondering if there's a more direct way?

Thanks in advance,

Sam

vg vgteam variation graph • 575 views
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2.2 years ago
glenn.hickey ▴ 250

vg find is probably the best. You may find the GFA output (vg view without the -j) easier to read or parse. Also note that it no longer requires an xg file, so you could use the same command on graph.vg too, and -c can be increased to pull larger subgraphs.

Python bindings to access the graph structure are in the works. They'll build on what was developed here: https://github.com/vgteam/odgi/pull/52

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