nodes were not found in the edge file

[alephreish]

I get the following fatal error message for the a test dataset (edges and nodes) after pressing "Create and open...":

Updating parameters
There are 183 nodes.
These are the Node properties: "Position, Group"
There are 183 nodes.
These are the Node properties: "Position, Group"
There are 140 edges in this network.
The properties of the edges:  "Similarity"
There are 183 nodes.
These are the Node properties: "Position, Group"
There are 140 edges in this network.
The properties of the edges:  "Similarity"
WARNING: 2 of the 183 nodes were not found in the edge file! Please filter them out using filter_data.py and rerun HivePlotter.

If you compare the lists, you see no orphans in the nodes file [filter_data.py is not functional, by the way :) ]. One of the edges somehow gets lost, because in reality there are 141 edges in the input file.

[sperez8]

Hi,

Thanks again for signalling a bug. It's been fixed now. The first edge wasn't being read for some reason.

As for filter_data, I'll test it with your data files and get back to you.

btw, nice plots!

Sarah

---

Sarah Perez Masters of Bioinformatics Candidate University of British Columbia T: 604-842-6751 http://munchaholic.wordpress.com/ https://github.com/sperez8/

On Tue, Sep 23, 2014 at 9:28 AM, har-wradim notifications@github.com wrote:

I get the following fatal error message for the a test dataset (edges https://gist.github.com/har-wradim/cf8ad29c48ce38e16a00#file-hive_test_edges and nodes https://gist.github.com/har-wradim/cf8ad29c48ce38e16a00#file-hive_test_nodes) after pressing "Create and open...":

Updating parameters There are 183 nodes. These are the Node properties: "Position, Group" There are 183 nodes. These are the Node properties: "Position, Group" There are 140 edges in this network. The properties of the edges: "Similarity" There are 183 nodes. These are the Node properties: "Position, Group" There are 140 edges in this network. The properties of the edges: "Similarity" WARNING: 2 of the 183 nodes were not found in the edge file! Please filter them out using filter_data.py and rerun HivePlotter.

If you compare the lists, you see no orphans in the nodes file [filter_data.py is not functional, by the way :) ]. One of the edges somehow gets lost, because in reality there are 141 edges in the input file.

— Reply to this email directly or view it on GitHub https://github.com/sperez8/HivePlotter/issues/3.

[sperez8]

Ah so filter_data was only working for comma separated files, not tab. That's probably the error you were getting? Otherwise, do let me know.

Also, thanks for sharing your files. The more files I test Hive Plotter with the better. Because your data isn't the kind of network Hive Plotter expects (it only has a pairs of nodes connected) it was breaking somethings and now Hive Plotter is more robust ;)

[alephreish]

Great!

filter_data was only working for comma separated files

Yes, and the paths were hard-coded :)

- nodeFile = "/Users/..."
- edgeFile = "/Users/..."
+ nodeFile, edgeFile = parse_args(*sys.argv[1:])

[sperez8]

Yes they were! I was still testing it out ;)