add script

fununifrac/reproducibility/assign_branch_lengths.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+#assigning branch lengths to using randomized method and deterministic method, using pw distance scaled 10 k 5
+#current dir = reproducibility
+
+kegg_tree_no_lengths="data/kegg_trees/kegg_ko00001_no_edge_lengths_filtered.txt"
+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 $out_dir -b ko00001
+python ../create_edge_lengths.py -d "../../fununifrac/reproducibility/"$ko_dm_file -e "d../../fununifrac/reproducibility/$kegg_tree_no_lengths" "../../fununifrac/reproducibility/$A_matrix" -b ko00001 -o "../../fununifrac/reproducibility/data/$rand_output" --force --distance