diff --git a/config/config.yaml b/config/config.yaml index 761a824a..6d2b4863 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -42,6 +42,9 @@ container_registry: # then myAlg will be run on (a=1,b=0.5),(a=1,b=0.75),(a=2,b=0.5), and (a=2,b=0,75). Pretty neat, but be # careful: too many parameters might make your runs take a long time. +# TODO: where does the dummy node argument go? +# i.e. where do i set dummy_mode = all, etc. + algorithms: - name: "pathlinker" params: @@ -56,6 +59,7 @@ algorithms: b: [5, 6] w: np.linspace(0,5,2) d: [10] + dummy_mode: ["file"] - name: "omicsintegrator2" params: @@ -100,24 +104,24 @@ algorithms: datasets: - # Labels can only contain letters, numbers, or underscores - label: data0 - node_files: ["node-prizes.txt", "sources.txt", "targets.txt"] + label: hivtest2 + node_files: ["modified_prize_05.txt", "dummy.txt"] # DataLoader.py can currently only load a single edge file, which is the primary network - edge_files: ["network.txt"] + edge_files: ["phosphosite-irefindex13.0-uniprot.txt"] # Placeholder other_files: [] # Relative path from the spras directory data_dir: "input" -gold_standards: - - - # Labels can only contain letters, numbers, or underscores - label: gs0 - node_files: ["gs_nodes0.txt"] - # edge_files: [] TODO: later iteration - data_dir: "input" - # List of dataset labels to compare with the specific gold standard dataset - dataset_labels: ["data0"] +# gold_standards: +# - +# # Labels can only contain letters, numbers, or underscores +# label: gs0 +# node_files: ["gs_nodes0.txt"] +# # edge_files: [] TODO: later iteration +# data_dir: "input" +# # List of dataset labels to compare with the specific gold standard dataset +# dataset_labels: ["data0"] # If we want to reconstruct then we should set run to true. # TODO: if include is true above but run is false here, algs are not run. @@ -160,4 +164,4 @@ analysis: # 'euclidean', 'manhattan', 'cosine' metric: 'euclidean' evaluation: - include: true + include: false diff --git a/input/dummy.txt b/input/dummy.txt new file mode 100644 index 00000000..535f50a7 --- /dev/null +++ b/input/dummy.txt @@ -0,0 +1,55 @@ +UBAC2_HUMAN +H37_HUMAN +PHF3_HUMAN +DDX52_HUMAN +HNRPK_HUMAN +Q5T5H1_HUMAN +ZC11A_HUMAN +TCPG_HUMAN +2A5E_HUMAN +CPNE2_HUMAN +HEYL_HUMAN +CAMP1_HUMAN +SVEP1_HUMAN +SPRL1_HUMAN +C9JFD3_HUMAN +THAP5_HUMAN +NCOR1_HUMAN +SKIL_HUMAN +A8YXX4_HUMAN +CO4A2_HUMAN +ZBTB3_HUMAN +MORC4_HUMAN +HIPK3_HUMAN +ZN200_HUMAN +TGFR1_HUMAN +Q2TU89_HUMAN +SUMO2_HUMAN +UBC9_HUMAN +AXIN1_HUMAN +RS27_HUMAN +UBP25_HUMAN +RN111_HUMAN +CBX4_HUMAN +B4E127_HUMAN +G4XH65_HUMAN +CPNE1_HUMAN +HDAC1_HUMAN +RNF4_HUMAN +SETB1_HUMAN +SMAD2_HUMAN +TRI62_HUMAN +FAF1_HUMAN +EF1G_HUMAN +AHNK_HUMAN +LRP1_HUMAN +UIMC1_HUMAN +B3KWV4_HUMAN +CDC27_HUMAN +RB_HUMAN +ZMYM2_HUMAN +WWP1_HUMAN +RU17_HUMAN +HIPK1_HUMAN +ZZEF1_HUMAN +SMAD4_HUMAN \ No newline at end of file diff --git a/input/modified_prize_05.txt b/input/modified_prize_05.txt new file mode 100644 index 00000000..bd3be433 --- /dev/null +++ b/input/modified_prize_05.txt @@ -0,0 +1,1124 @@ +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 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+FYV1_HUMAN 1.0142648815187705 +A0A1B0GTN9_HUMAN 1.0109627568592905 +SRA1_HUMAN 1.0096828639556032 +UIF_HUMAN 1.0096828639556032 +JHD2C_HUMAN 1.0094992600098456 +APTX_HUMAN 1.0084603804047647 +J3KQL8_HUMAN 1.0077614527324577 +AXIN1_HUMAN 1.005808582397118 +RTN4_HUMAN 1.0051920614387837 +J3KR72_HUMAN 1.0037550381491789 +PARP6_HUMAN 1.003196032647505 +T184C_HUMAN 1.0022879202716266 diff --git a/spras/omicsintegrator1.py b/spras/omicsintegrator1.py index 90283475..ad47aeed 100644 --- a/spras/omicsintegrator1.py +++ b/spras/omicsintegrator1.py @@ -49,8 +49,6 @@ def write_conf(filename=Path('config.txt'), w=None, b=None, d=None, mu=None, noi class OmicsIntegrator1(PRM): required_inputs = ['prizes', 'edges', 'dummy_nodes'] - #TODO: TEST !!!!! + test files?? - @staticmethod def generate_inputs(data, filename_map): """ @@ -77,10 +75,10 @@ def generate_inputs(data, filename_map): # Omics Integrator already gives warnings for strange prize values, so we won't here node_df.to_csv(filename_map['prizes'],sep='\t',index=False,columns=['NODEID','prize'],header=['name','prize']) - print("DATA: NODE TABLE") - print(data.node_table.head()) - print("NODE DF") - print(node_df.head()) + # print("DATA: NODE TABLE") + # print(data.node_table[data.node_table['dummy']==True]) + # print("NODE DF") + # print(node_df.head()) # Get network file edges_df = data.get_interactome() @@ -91,10 +89,11 @@ def generate_inputs(data, filename_map): header=['protein1','protein2','weight','directionality']) # creates the dummy_nodes file - if node_df.contains_node_columns('dummy'): - dummy_df = node_df[node_df['dummy'] == True] + if 'dummy' in data.node_table.columns: + dummy_df = data.node_table[data.node_table['dummy'] == True] # save as list of dummy nodes - dummy_df.to_csv(filename_map['dummy_nodes'], sep='\t', index=False, columns=['NODEID', 'dummy'], header=['NODEID', 'dummy']) + # dummy_df.to_csv(filename_map['dummy_nodes'], sep='\t', index=False, columns=['NODEID', 'dummy'], header=['NODEID', 'dummy']) + 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: