Consolidate common functions in an IO util

TobiasRubel / Pathway-Reconstruction-Tools

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Consolidate common functions in an IO util #2

Open annaritz opened 4 years ago

annaritz commented 4 years ago

Common file input/output functions can be put into their on fileio.py module. For now I copied your df_to_graph() function and src_sink() function from PerfectLinker to my code.

TobiasRubel commented 4 years ago

Good idea. Do you suggest we throw fileio.py into an existing directory (maybe misc?), or make a new utils directory.

annaritz commented 4 years ago

Maybe make a utils directory. Some other notes:

The graph can be weighted or unweighted -- the new methods I added also assume a cost attribute to every edge, which is the negative log of the weights. Specifically, for weight w,
```
cost = -math_log(max([0.000000001, w]))/math_log(10))
```
I"ve added this to the df_to_graph() functions in ShortestPaths, BowtieBUilder, and ResponseNet.
get_labeled_nodes() -- can sources and sinks be a set instead of a list? BowTieBUilder requires a set.