major environment reduction

docs/notes/Notes_development.md

@@ -22,15 +22,22 @@
 
     - Takes the form of X*, or proposed{issue} to follow UShER.
 
-## To DO
-
-### Priority
-
 1. Consolidate lineage assignments into a single column.
 
     - sc2rf takes priority if a single lineage is identified.
     - usher is next, to resolve ties or if sc2rf had no lineage.
-    - finally, we use nextclade... at all?
+
+1. Slim down the conda environment and remove unnecessary programs.
+
+    - `augur`
+    - `seaborn`
+    - `snipit`
+    - `bedtools`
+    - Comment out `git` and `pre-commit`.
+
+## To DO
+
+### Priority
 
 1. Add documentation to the report.
 

scripts/usher_collapse.py

@@ -3,9 +3,6 @@
 import filecmp
 import shutil
 import os
-import json
-from Bio import Phylo
-from augur.utils import json_to_tree
 
 NO_DATA_CHAR = "NA"
 
@@ -127,13 +124,6 @@ def main(
         out_path = os.path.join(outdir, "subtree_{}.json".format(i))
         shutil.copyfile(in_path, out_path)
 
-        # Convert to newick
-        out_path_nwk = os.path.join(outdir, "subtree_{}.nwk".format(i))
-        with open(out_path) as infile:
-            tree_json = json.load(infile)
-        tree = json_to_tree(tree_json)
-        Phylo.write(tree, out_path_nwk, "newick")
-
         # Strain List
         out_path_strains = os.path.join(outdir, "subtree_{}.txt".format(i))
         strains_list = [t.name for t in tree.get_terminals()]