debugging a bug I added doing the pep8

KatyBrown · May 14, 2024 · 8667a73 · 8667a73
1 parent d294923
commit 8667a73
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Showing 2 changed files with 41 additions and 28 deletions.
diff --git a/CIAlign/consensusSeq.py b/CIAlign/consensusSeq.py
@@ -660,11 +660,21 @@ def calcConservationAli(alignment, typ):
     Calculate alignment conservation as the heights the letters would
     be in a sequence logo.
 
+    Parameters
+    -----------
     alignment: np.array
         The alignment stored as a numpy array
 
     typ: str
         nt or aa
+
+    Returns
+    -------
+    heights: list
+        A list containing the letter height for each column
+    ents: list
+        A list containing the entropy calculated for each column
+    
     '''
     alignment_width = len(alignment[0, :])
     seq_count = len(alignment[:, 0])
@@ -697,25 +707,26 @@ def compareAlignmentConsensus(arr):
     A numpy array stored as new_arr, which is a boolean array
     comparing the arr to its consensus.
     '''
-    consensus, _ = np.array(findConsensus(arr, ''))
+    consensus, _ = np.array(findConsensus(arr, '',
+                                          consensus_type='majority_nongap'))
     bool_array = np.array([])
     bool_arrL = np.empty(dtype=bool, shape=(0, len(consensus)))
     # declares the numpy arrays
     for e in range(1, (len(arr[:, 0])+1)):
         # iterates over the rows of the sequences
         z = e - 1
-    for i in range(1, (len(arr[0, :])+1)):
-        # iterates over the columns of the sequences
-        x = i - 1
-        if arr[z, x] == consensus[x]:
-            # verifies if the current value being iterated is equal to
-            # the equivalent value inline with the consensus
-            bool_array = np.append(bool_array, [True], axis=None)
-        else:
-            bool_array = np.append(bool_array, [False], axis=None)
-    bool_arrL = np.vstack([bool_arrL,
-                           bool_array])
-    bool_array = np.array([])
+        for i in range(1, (len(arr[0, :])+1)):
+            # iterates over the columns of the sequences
+            x = i - 1
+            if arr[z, x] == consensus[x]:
+                # verifies if the current value being iterated is equal to
+                # the equivalent value inline with the consensus
+                bool_array = np.append(bool_array, [True], axis=None)
+            else:
+                bool_array = np.append(bool_array, [False], axis=None)
+        bool_arrL = np.vstack([bool_arrL,
+                               bool_array])
+        bool_array = np.array([])
     new_arr = copy.deepcopy(bool_arrL)
     new_arr = bool_arrL.astype(bool)
     # returns the new boolean array containing the verified alignment

diff --git a/CIAlign/runCIAlign.py b/CIAlign/runCIAlign.py
@@ -835,9 +835,11 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
             print("Plotting mini alignment for input")
         outf = "%s_input.%s" % (args.outfile_stem, args.plot_format)
         miniAlignments.drawMiniAlignment(orig_arr, orig_nams, log,
-                                         outf, typ, args.plot_dpi,
-                                         False, args.plot_width,
-                                         args.plot_height,
+                                         outf, typ,
+                                         dpi=args.plot_dpi,
+                                         title=False,
+                                         width=args.plot_width,
+                                         height=args.plot_height,
                                          force_numbers=fn,
                                          palette=args.palette)
     # Mini alignment of CIAlign output
@@ -850,19 +852,19 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
         if not args.plot_keep_numbers:
             miniAlignments.drawMiniAlignment(arr, nams, log,
                                              outf, typ,
-                                             args.plot_dpi,
-                                             False,
-                                             args.plot_width,
-                                             args.plot_height,
+                                             dpi=args.plot_dpi,
+                                             title=False,
+                                             width=args.plot_width,
+                                             height=args.plot_height,
                                              force_numbers=fn,
                                              palette=args.palette)
         else:
             miniAlignments.drawMiniAlignment(arr, nams, log,
                                              outf, typ,
-                                             args.plot_dpi,
-                                             False,
-                                             args.plot_width,
-                                             args.plot_height,
+                                             dpi=args.plot_dpi,
+                                             title=False,
+                                             width=args.plot_width,
+                                             height=args.plot_height,
                                              orig_nams=orig_nams,
                                              keep_numbers=True,
                                              force_numbers=fn,
@@ -876,10 +878,10 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
         outf = "%s_markup.%s" % (args.outfile_stem, args.plot_format)
         miniAlignments.drawMiniAlignment(orig_arr, orig_nams, log,
                                          outf, typ,
-                                         args.plot_dpi,
-                                         False,
-                                         args.plot_width,
-                                         args.plot_height,
+                                         dpi=args.plot_dpi,
+                                         title=False,
+                                         width=args.plot_width,
+                                         height=args.plot_height,
                                          markup=True,
                                          markupdict=markupdict,
                                          force_numbers=fn,