cytoscape

Legacy Cytoscape Attributes Format not importing


Reading the documentation, section 8.2 here: http://manual.cytoscape.org/en/stable/Node_and_Edge_Column_Data.html

The docs state that the legacy attributes format is still supported in cytoscape 3.8. I have a legacy attribute file in the following format:

LinkerHeats
PKC = 0.05283780217268941
CDKN1B = 0.9230103703466229
RAS = 0.001407567832956147
BRCA1 = 0.0005058090659030887

However when I try to import the file using File -> Import -> Table from file... I cannot find a way for cytoscape to recognize anything but a single column, and it throws an error:

Table must have more than one column. Please check the selected delimeters and columns.

The import dialog is shown:

enter image description here

I can manually convert the file to CSV and import it, but it's a bit annoying to need the conversion utility since the docs suggest this should work.


Solution

  • I'm not sure why, but I was able to import that file by deleting the first line of the file (e.g. the column label) and using "=" as the delimiter. Obviously you have to rename the column before the import, but I was able to get it to work without having to convert it. The documentation is clearly wrong and we'll make sure to remove that comment as I think we removed support for that format several releases ago when we cleaned up our File menu.