Load PSI-MI file from command line?

[Florian Breitwieser]

Hello,

I'm trying to find out how to webstart a psi-mi file from Cytoscape. I
searched in the wiki and the net, and did not come up with a solution.

>>-N,--network <file>
>>This option is used to load all types of network files. SIF, GML, and XGMML files can all be loaded using the -N option.

The -N argument does not work, as specified in the documentation it
does not load PSI-MI files.. Is there another way?

Best,
Florian

[Mike Smoot]

This should work.  Can you send the file you're having problems with as well as the exact command line you're typing out?

thanks,
Mike

--
____________________________________________________________
Michael Smoot, Ph.D.              
UCSD Department of Medicine
tel: 858-822-4756

[Florian Breitwieser]

Sure. The psimi-xml file is a recent one from IntAct. Loading it via 'File' > 'Import' > 'Network (multiple file types)' works without problems.

Cytoscape version: v2.6.2

Command: Cytoscape -N 17627824.xml

Error message:
cytoscape.CytoscapeInit[ERROR]: Couldn't load network from file '17627824.xml': Couldn't read specified file. Couldn't read specified file. java.lang.RuntimeException: Couldn't read specified file. at cytoscape.Cytoscape.createNetwork(Cytoscape.java:1374) at cytoscape.Cytoscape.createNetworkFromFile(Cytoscape.java:1332) at cytoscape.CytoscapeInit.loadNetworks(CytoscapeInit.java:597) at cytoscape.CytoscapeInit.init(CytoscapeInit.java:279) at cytoscape.CyMain. (CyMain.java:158) at cytoscape.CyMain.main(CyMain.java:122)

Thanks,
Florian

[Michi]

Try giving the absolute path for the file.

It worked fine for me on windows xp

Cytoscape.exe -N I:\17627824.xml


Michael

[Florian Breitwieser]

Wow, that was an easy fix :). Yeah, this way it is working for me, too.

Thanks a lot!