visualizing the singletons about big-scape HOT 2 OPEN

Hi,

Yes, I think it's the same case. If I remember correctly, the singletons are always shown in the interactive output, but not on the .network file unless you use --include_singletons.

It should be easy to extract these singletons from the .networks file, as their first two columns are repeated (i.e. they are only "connected" to themselves). In Python this should be something like:

#!/usr/bin/env python3
"""
Call this script as
python [name of script].py <bigscape.network file>
"""

from sys import argv

with open(argv[1]) as nt, open("singletons.network", "w") as sgl:
    sgl.write(nt.readline())
    for line in nt:
        node1, node2 = line.split("\t")[:2]
        if node1 == node2:
            sgl.write(line)

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