fixed addition of extra AA, added a function to AminoAcid class for testing

Author: evelyn-schmidt

scripts/color_peptides51mer.py

@@ -17,6 +17,15 @@ def __init__(self, nucleotide, bold, color, underline, large, position, open_tag
         self.open_tag = open_tag
         self.close_tag = close_tag
 
+    def view(self):
+        print("Nucleotide: ", self.nucleotide)
+        print("Open Tag: ", self.open_tag)
+        print("Close Tag: ", self.close_tag)
+        print("Bold: ", self.bold)
+        print("Color: ",self.color)
+        print("Underline: ", self.underline)
+        print("Large: ", self.large)
+
 # ---- PARSE ARGUMENTS -------------------------------------------------------
 # Parses command line arguments
 # Enables user help
@@ -178,7 +187,7 @@ def set_span_tags(peptide_sequence):
             nucleotide.open_tag = True
 
             if inside_span:
-                nucleotide.close_tag = True # only if its isnide a span tag
+                nucleotide.close_tag = True # only if its inside a span tag
             else:
                 nucleotide.close_tag = False
 
@@ -202,9 +211,7 @@ def create_stylized_sequence(peptide_sequence):
             if nucleotide.close_tag:
                 new_string += '</span>'
 
-
             if nucleotide.open_tag:
-
                 new_string += '<span style="'
                 if nucleotide.bold:
                     new_string += 'font-weight:bold;'
@@ -216,9 +223,6 @@ def create_stylized_sequence(peptide_sequence):
                      new_string += 'font-size:105%;'
                 new_string += '">'
                 new_string += nucleotide.nucleotide
-
-            if not nucleotide.large and not nucleotide.bold and not nucleotide.color and not nucleotide.underline:
-                new_string += nucleotide.nucleotide
         else:
             new_string += nucleotide.nucleotide
     return(new_string)   
@@ -305,6 +309,7 @@ def main():
 
             set_span_tags(peptide_sequence) # pass by reference
 
+            print(row['51mer ID'])
             new_string = create_stylized_sequence(peptide_sequence)
 
             next_td_tags[2].string = new_string