documented research per algorithm as docstrings per class for the alg…

…orithms in master

src/domino.py

@@ -11,7 +11,15 @@
 ID_PREFIX = 'ENSG0'
 ID_PREFIX_LEN = len(ID_PREFIX)
 
-
+"""
+Domino will construct a fully undirected graph from the provided input file
+- in the algorithm, it uses nx.Graph()
+
+Expected raw input format: 
+Interactor1     ppi     Interactor2
+- the expected raw input file should have node pairs in the 1st and 3rd columns, with a 'ppi' in the 2nd column
+- it can include repeated and bidirectional edges
+"""
 class DOMINO(PRM):
     required_inputs = ['network', 'active_genes']
 

src/meo.py

@@ -46,6 +46,16 @@ def write_properties(filename=Path('properties.txt'), edges=None, sources=None,
         # Do not need csp.phase, csp.gen.file, or csp.sol.file because MAXCSP is not supported
 
 
+"""
+MEO can support partially directed graphs
+
+Expected raw input format: 
+Interactor1   pp/pd   Interactor2   Weight
+- the expected raw input file should have node pairs in the 1st and 3rd columns, with a directionality in the 2nd column and the weight in the 4th column
+- it use pp for undirected edges and pd for directed edges
+- it cannot include repeated and bidirectional edges
+- there is a chance MRO assumes that it should just be an undirected edge instead
+"""
 class MEO(PRM):
     required_inputs = ['sources', 'targets', 'edges']
 

src/mincostflow.py

@@ -7,7 +7,16 @@
 
 __all__ = ['MinCostFlow']
 
-
+"""
+MinCostFlow deals with fully directed graphs
+- OR Tools MCF is designed for directed graphs
+- when an edge (arc), it has a source and target node, so flow it only allowed to moced from source to the target
+
+Expected raw input format: 
+Interactor1  Interactor2   Weight
+- the expected raw input file should have node pairs in the 1st and 2nd columns, with the weight in the 3rd column
+- it can include repeated and bidirectional edges
+"""
 class MinCostFlow (PRM):
     required_inputs = ['sources', 'targets', 'edges']
 

src/omicsintegrator1.py

@@ -35,7 +35,17 @@ def write_conf(filename=Path('config.txt'), w=None, b=None, d=None, mu=None, noi
         f.write('processes = 1\n')
         f.write('threads = 1\n')
 
+"""
+Omics Integrator 1 will construct works with partially directed graphs
+- it takes in the universal input directly 
 
+Expected raw input format: 
+Interactor1    Interactor2   Weight    Direction
+- the expected raw input file should have node pairs in the 1st and 2nd columns, with a weight in the 3rd column and directionality in the 4th column
+- it can include repeated and bidirectional edges
+- it uses 'U' for undirected edges and 'D' for directed edges
+
+"""
 class OmicsIntegrator1(PRM):
     required_inputs = ['prizes', 'edges']
 

src/omicsintegrator2.py

@@ -9,7 +9,16 @@
 
 __all__ = ['OmicsIntegrator2']
 
-
+"""
+Omics Integrator 2 will construct a fully undirected graph from the provided input file
+- in the algorithm, it uses nx.Graph() objects, which are undirected
+- uses a pcst_fast solver which supports undirected graphs
+
+Expected raw input format: 
+Interactor1   Interactor2   Weight
+- the expected raw input file should have node pairs in the 1st and 2nd columns, with a weight in the 3rd column
+- it can include repeated and bidirectional edges
+"""
 class OmicsIntegrator2(PRM):
     required_inputs = ['prizes', 'edges']
 

src/pathlinker.py

@@ -8,6 +8,15 @@
 
 __all__ = ['PathLinker']
 
+"""
+Pathlinker will construct a fully directed graph from the provided input file
+- an edge is represented with a head and tail node, which represents the direction of the interation between two nodes
+
+Expected raw input format: 
+Interactor1   Interactor2   Weight
+- the expected raw input file should have node pairs in the 1st and 2nd columns, with a weight in the 3rd column
+- it can include repeated and bidirectional edges
+"""
 class PathLinker(PRM):
     required_inputs = ['nodetypes', 'network']