cleaned up user outputs, cleaned up barcoding

freyja/_cli.py

@@ -64,7 +64,9 @@ def update():
     df_barcodes = convert_to_barcodes(df)
     df_barcodes = reversion_checking(df_barcodes)
     df_barcodes.to_csv(os.path.join(locDir, 'data/usher_barcodes.csv'))
-    # TODO: delete files generated along the way
+    # delete files generated along the way that aren't needed anymore
+    os.remove(lineagePath)
+    os.remove(os.path.join(locDir, "data/public-latest.all.masked.pb.gz"))
 
 
 @cli.command()

freyja/sample_deconv.py

@@ -41,7 +41,7 @@ def build_mix_and_depth_arrays(fn, depthFn, muts):
 
 def reindex_dfs(df_barcodes, mix, depths):
     # first, drop Nextstrain clade names.
-    nxNames = ['20A', '20C', '20D', '20H(Beta,V2)', '21C(Epsilon)']
+    nxNames = df_barcodes.index[df_barcodes.index.str[0].str.isdigit()]
     dropList = set(nxNames) & set(df_barcodes.index)
     df_barcodes = df_barcodes.drop(index=dropList)
     # reindex everything to match across the dfs

freyja/updates.py

@@ -13,7 +13,6 @@ def download_tree():
 
 
 def convert_tree():
-    print('Converting tree into barcodes',)
     locDir = os.path.abspath(os.path.join(os.path.realpath(__file__),
                                           os.pardir))
     treePath = os.path.join(locDir, "data/public-latest.all.masked.pb.gz")
@@ -25,7 +24,6 @@ def convert_tree():
 def get_curated_lineage_data():
     locDir = os.path.abspath(os.path.join(os.path.realpath(__file__),
                                           os.pardir))
-    print('Downloading an updated curated lineage set from outbreak.info')
     url2 = "https://raw.githubusercontent.com/outbreak-info/outbreak.info/"\
            "master/web/src/assets/genomics/curated_lineages.json"
     urllib.request.urlretrieve(url2,