diff --git a/config/config.yaml b/config/config.yaml index a2428077..6b1949fa 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -45,7 +45,7 @@ container_registry: algorithms: - name: "pathlinker" params: - include: false + include: true run1: k: range(100,201,100) @@ -56,11 +56,11 @@ algorithms: b: [5, 6] w: np.linspace(0,5,2) d: [10] - dummy_mode: ["terminals"] + dummy_mode: ["terminals"] - name: "omicsintegrator2" params: - include: false + include: true run1: b: [4] g: [0] @@ -70,7 +70,7 @@ algorithms: - name: "meo" params: - include: false + include: true run1: max_path_length: [3] local_search: ["Yes"] @@ -78,18 +78,18 @@ algorithms: - name: "mincostflow" params: - include: false + include: true run1: flow: [1] # The flow must be an int capacity: [1] - name: "allpairs" params: - include: false + include: true - name: "domino" params: - include: false + include: true run1: slice_threshold: [0.3] module_threshold: [0.05] diff --git a/input/modified_prize_05.txt b/input/modified_prize_05.txt deleted file mode 100644 index bd3be433..00000000 --- a/input/modified_prize_05.txt +++ /dev/null @@ -1,1124 +0,0 @@ -NODEID prize -B0YIW2_HUMAN 5.029365599650682 -HTF4_HUMAN 4.582688156260696 -FETUA_HUMAN 4.027455886706566 -HBA_HUMAN 3.955817065609741 -KCRM_HUMAN 3.885427876677981 -B7ZKJ8_HUMAN 3.885427876677981 -H4_HUMAN 3.885427876677981 -FBLN1_HUMAN 3.885427876677981 -H3BLZ8_HUMAN 3.737659276683696 -MMTA2_HUMAN 3.645611351503717 -CL16A_HUMAN 3.645611351503717 -ALBU_HUMAN 3.495543593199523 -UBAC2_HUMAN 3.4400540448812222 -H37_HUMAN 3.4400540448812222 -PHF3_HUMAN 3.324208299637505 -DDX52_HUMAN 3.324208299637505 -TBA1B_HUMAN 3.324208299637505 -HNRPK_HUMAN 3.3188421301096285 -Q5T5H1_HUMAN 3.3188421301096285 -ZC11A_HUMAN 3.3188421301096285 -EPB41_HUMAN 3.3010716433184752 -LARP1_HUMAN 3.3010716433184752 -GLYR1_HUMAN 3.291925211826148 -ZC3HD_HUMAN 3.291925211826148 -TRFE_HUMAN 3.2382104940279395 -A0A0A0MTS7_HUMAN 3.238051370574229 -RL34_HUMAN 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edges_df.to_csv(filename_map['edges'],sep='\t',index=False, columns=['Interactor1','Interactor2','Weight','Direction'], header=['protein1','protein2','weight','directionality']) - + # creates the dummy_nodes file if 'dummy' in data.node_table.columns: - dummy_df = data.node_table[data.node_table['dummy'] == True] + dummy_df = data.node_table[data.node_table['dummy'] == True] # save as list of dummy nodes dummy_df.to_csv(filename_map['dummy_nodes'], index=False, columns=['NODEID'], header=None) else: - # create empty dummy file - with open(filename_map['dummy_nodes'], mode='w') as file: + # create empty dummy file + with open(filename_map['dummy_nodes'], mode='w'): pass @@ -129,7 +129,7 @@ def run(edges=None, prizes=None, dummy_nodes=None, dummy_mode=None, mu_squared=N volumes.append(bind_path) # 4 dummy mode possibilities: - # 1. terminals -> connect the dummy node to all nodes that have been assigned prizes + # 1. terminals -> connect the dummy node to all nodes that have been assigned prizes # 2. all -> connect the dummy node to all nodes in the interactome i.e. full set of nodes in graph # 3. others -> connect the dummy node to all nodes that are not terminal nodes i.e. nodes w/o prizes # 4. file -> custom nodes - connect the dummy node to a specific list of nodes provided in a file @@ -160,7 +160,7 @@ def run(edges=None, prizes=None, dummy_nodes=None, dummy_mode=None, mu_squared=N '--msgpath', '/OmicsIntegrator/msgsteiner-1.3/msgsteiner', '--outpath', mapped_out_dir, '--outlabel', 'oi1'] - + # add the dummy mode argument if dummy_mode is not None and dummy_mode: # for custom dummy modes, add the file