No edges in the reimported network

[Michel Michaels]

Hi,

there is no edges in the reimported network.

I done the following steps:

1)  Export network to file (sif)

2)  Import network from file (sif)

Edges are missing.

Should I consider some settings ?

Thanks,

Michel

[Alex Pico]

Here’s a working example:

1. Open sample session file: Yeast Perturbation

2. File > Expor > Network to File (save new sif file)

3. File > Import > Network from File (point to saved sif file)

Does this work for you?

Can you provide files and steps to reproduce the case that does not work for you?

 - Alex

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[Michel Michaels]

Hi Alex,

thanks for your time spent for me.

Yes, the "working example"is forking for me too. 

In my case I exported  ( export.png ) the network from subtasks.cys ( attached ) , the result is subtask.sif (attached). Then I imported the subtask.sif  ( imported_network.png )  - no edges.

Thanks in advace,

Michel

On Saturday, January 12, 2019 at 8:59:22 PM UTC+1, Alex Pico wrote:

Here’s a working example:

1. Open sample session file: Yeast Perturbation

2. File > Expor > Network to File (save new sif file)

3. File > Import > Network from File (point to saved sif file)

Does this work for you?

Can you provide files and steps to reproduce the case that does not work for you?

 - Alex

On Jan 11, 2019, at 11:56 PM, Michel Michaels <michel7...@gmail.com> wrote:

Hi,

there is no edges in the reimported network.

I done the following steps:

1)  Export network to file (sif)

2)  Import network from file (sif)

Edges are missing.

Should I consider some settings ?

Thanks,

Michel

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[Alex Pico]

Thanks for the files!  You found a bug… congratulations! :)

Seriously, this is an odd one. It turns out that the first line of your exported SIF only have one column (because the first node listed doesn’t have interactions). So, the SIF importer tries to be “smart” and guesses that you are only importing nodes, no interactions. It proceeds to read in only the first column. This is why you have no interactions AND fewer nodes.

If you add a couple tabs into the first line (representing columns 2 and 3), then the file is imported correctly. See attached.

I will file this as a bug. Not sure what or when the final fix will be in, however. This happens when importing tables as well. The first line is used to establish the format.

Work arounds in the meantime… export/import as .xgmml instead of .sif.  That is a more explicit format. Will that work for you?

 - Alex

[Michel Michaels]

Hi Alex,

thanks for analysis and for alternate ways to fulfill my requirements.   I checked them, both of them are working.

Regards,

Michel