modify arguments

fununifrac/reproducibility/assign_branch_lengths.sh

@@ -8,12 +8,10 @@ ko_dm_file="data/pairwise_distances/KOs_sketched_scaled_10_k_5"
 label_file="data/pairwise_distances/KOs_sketched_scaled_10_k_5.labels.txt"
 out_dir="data/kegg_trees"
 deterministic_output="data/kegg_trees/kegg_ko00001_scaled_10_k_5_assigned_positivity_enforced.txt"
-A_matrix="data/kegg_trees/fununifrac_A.npz"
-rand_output="data/kegg_trees/kegg_ko00001_randomized_method.txt"
 
 #deterministic method
 #python real_data_branch_assignment.py -e $kegg_tree_no_lengths -dm $ko_dm_file -l $label_file -s $deterministic_output
 
 #randomized method
 #python ../create_edge_matrix.py -e $kegg_tree_no_lengths -d $ko_dm_file -o $out_dir -b ko00001
-python ../compute_edges.py -d "../../fununifrac/reproducibility/"$ko_dm_file -e "../../fununifrac/reproducibility/$kegg_tree_no_lengths" -b ko00001 -o "../../fununifrac/reproducibility/data/$rand_output" --distance
+python ../compute_edges.py -d "../../fununifrac/reproducibility/"$ko_dm_file -e "../../fununifrac/reproducibility/$kegg_tree_no_lengths" -b ko00001 -o "../../fununifrac/reproducibility/data/$" -i kegg_ko00001_randomized_method --distance