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fraenkel-lab / OmicsIntegrator

This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.
http://fraenkel.mit.edu/omicsintegrator
BSD 2-Clause "Simplified" License
31 stars 21 forks source link

Directed edges bug #16

Closed aabaker99 closed 8 years ago

aabaker99 commented 8 years ago

While working on some tests I found that a vertex with no out degree that is the tail of a directed edge is excluded from the PCSF optimization problem. Vertices are meant to be excluded if they are not part of the interactome. The previous check for "part of the interactome" only checked the head of directed edges and not the tail. The PR adds checks for the tail.

Passing CI here: https://travis-ci.org/aabaker99/OmicsIntegrator/builds/144186558

agitter commented 8 years ago

@aabaker99 and I already discussed these tests and this bug, so I'll review the pull request. I should be able to look it over next week.

agitter commented 8 years ago

I'm merging this pull request. The new test_util functions will be great for writing more unit tests. I will follow up with a small modification to the configuration file writing function so that parameters that can take floating point values are written accordingly.