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thpar / diffany

Diffany is an open-source toolbox for calculating and visualizing differential networks.
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[CLOSED] clean input before writing #189

Closed diffany-admin closed 9 years ago

diffany-admin commented 9 years ago

Issue by svlandeg Mon Sep 8 15:01:32 2014

The osmotic network data does not seem to be properly cleaned before writing to file, e.g. few symmetrical PPI edges are recorded both as source-target as well as target-source.

This should be cleaned before writing, to avoid redundant processing times.

diffany-admin commented 9 years ago

Comment by svlandeg Tue Sep 9 12:18:36 2014

e.g. in osmotic reference network: at2g18790 at2g20180 validated_ppi symmetrical 1.0 affirmative at2g20180 at2g18790 validated_ppi symmetrical 1.0 affirmative

There is also this (which shouldn't affect things, but perhaps does): at2g20180 at2g18790 activation asymmetrical 1.0 affirmative

diffany-admin commented 9 years ago

Comment by svlandeg Tue Sep 9 13:10:14 2014

fixed by altering NetworkCleaning.cleanEdges to have separate directed_pairs and symmetrical_pairs

diffany-admin commented 9 years ago

Comment by svlandeg Tue Sep 9 14:48:28 2014

this broke junit tests!