GMYC_spec -> Delim_spec for clarity

tokebe · Feb 19, 2021 · 9acd772 · 9acd772
1 parent e4ed159
commit 9acd772
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/niclassify/core/StandardProgram.py b/niclassify/core/StandardProgram.py
@@ -204,7 +204,7 @@ def mp_delim(arg):
 
     # rename delims with order prefix
     delim = utilities.get_data(arg[3])
-    delim["GMYC_spec"] = arg[0] + delim["GMYC_spec"].astype(str)
+    delim["Delim_spec"] = arg[0] + delim["Delim_spec"].astype(str)
     delim.to_csv(arg[3], sep="\t", index=False)
 
 
@@ -472,7 +472,7 @@ def check_r_working(self, cb=None):
         if cb is not None:
             cb()
         return False
-        
+
     def check_single_split(self, data, cb=None):
         """
         Check if splitting data by taxon split level would return subsets of

diff --git a/niclassify/core/scripts/create_measures.R b/niclassify/core/scripts/create_measures.R
@@ -58,9 +58,9 @@ dnaDist <- melt(dnaDist)
 ### Add species groups to distance table ###
 dnaDist <- dnaDist %>%
   left_join(speciesNames, by = c("Var1" = "sample_name")) %>%
-  rename(Var1_group = GMYC_spec) %>%
+  rename(Var1_group = Delim_spec) %>%
   left_join(speciesNames, by = c("Var2" = "sample_name")) %>%
-  rename(Var2_group = GMYC_spec)
+  rename(Var2_group = Delim_spec)
 
 ### Create summary statistics ###
 dnaDistAggregated <- dnaDist %>%
@@ -80,7 +80,7 @@ dnaDistAggregated <- dnaDist %>%
 
 ### Join with sample names in preparation for output ###
 groups_metrics <- dnaDistAggregated %>%
-  right_join(speciesNames, by = c("Var1_group" = "GMYC_spec")) %>%
+  right_join(speciesNames, by = c("Var1_group" = "Delim_spec")) %>%
   rename(species_group = Var1_group)
 
 
@@ -91,9 +91,9 @@ aaDist <- melt(aaDist)
 ### Add species groups to distance table ###
 aaDist <- aaDist %>%
   left_join(speciesNames, by = c("Var1" = "sample_name")) %>%
-  rename(Var1_group = GMYC_spec) %>%
+  rename(Var1_group = Delim_spec) %>%
   left_join(speciesNames, by = c("Var2" = "sample_name")) %>%
-  rename(Var2_group = GMYC_spec)
+  rename(Var2_group = Delim_spec)
 
 ### Create summary statistics ###
 aaDistAggregated <- aaDist %>%
@@ -124,9 +124,9 @@ if (!is.atomic(seqKaKs)) {
   ### Add species groups to distance table ###
   kaDist <- kaDist %>%
     left_join(speciesNames, by = c("Var1" = "sample_name")) %>%
-    rename(Var1_group = GMYC_spec) %>%
+    rename(Var1_group = Delim_spec) %>%
     left_join(speciesNames, by = c("Var2" = "sample_name")) %>%
-    rename(Var2_group = GMYC_spec)
+    rename(Var2_group = Delim_spec)
 
   ### Create summary statistics ###
   kaDistAggregated <- kaDist %>%
@@ -156,9 +156,9 @@ if (!is.atomic(seqKaKs)) {
   ### Add species groups to distance table ###
   ksDist <- ksDist %>%
     left_join(speciesNames, by = c("Var1" = "sample_name")) %>%
-    rename(Var1_group = GMYC_spec) %>%
+    rename(Var1_group = Delim_spec) %>%
     left_join(speciesNames, by = c("Var2" = "sample_name")) %>%
-    rename(Var2_group = GMYC_spec)
+    rename(Var2_group = Delim_spec)
 
   ### Create summary statistics ###
   ksDistAggregated <- ksDist %>%

diff --git a/niclassify/core/utilities/general_utils.py b/niclassify/core/utilities/general_utils.py
@@ -39,7 +39,7 @@
 }
 
 with pkg_resources.path(config, _icon_to_use[PLATFORM]) as p:
-    PROGRAM_ICON = str(p) if platform == 'Windows' else "@" + str(p)
+    PROGRAM_ICON = str(p) if PLATFORM == 'Windows' else "@" + str(p)
 
 if PLATFORM == "Windows":
     with pkg_resources.open_text(config, "rloc.txt") as rloc: