Fixed bug where searching left would break if the final correct prime…

…r sequence was identified but was not the last primer.
jackwadden · Jul 27, 2021 · cd61a59 · cd61a59
1 parent 00319eb
commit cd61a59
Showing 1 changed file with 16 additions and 1 deletion.
diff --git a/lamprey.py b/lamprey.py
@@ -118,7  118,10 @@ def __init__(self, primer_set_filename):
                     self.primer_dict[primer_name[:-1]] = rc(primer_string)
                 else:
                     self.primer_dict[primer_name] = primer_string
-
 
 
             print(self.fwd_primer_order)
             print(self.rev_primer_order)
 #########################
 class Alignment:
     '''
@@ -404,6  407,10 @@ def setPrimerColor(primer_string):
         color = '\u001b[38;5;4;7m'
     elif primer_string == 'F2c':
         color = '\u001b[38;5;4m'
     elif primer_string == 'F3':
         color = '\u001b[38;5;4;7m'
     elif primer_string == 'F3c':
         color = '\u001b[38;5;4m'
     elif primer_string == 'F1':
         color = '\u001b[38;5;75;7m'
     elif primer_string == 'F1c':
@@ -412,6  419,10 @@ def setPrimerColor(primer_string):
         color = '\u001b[38;5;1;7m'
     elif primer_string == 'B2c':
         color = '\u001b[38;5;1m'
     elif primer_string == 'B3':
         color = '\u001b[38;5;1;7m'
     elif primer_string == 'B3c':
         color = '\u001b[38;5;1m'
     elif primer_string == 'B1':
         color = '\u001b[38;5;204;7m'
     elif primer_string == 'B1c':
@@ -636,6  647,10 @@ def extractAmpliconAroundTarget(primer_set, alignments, target):
         else:
             primer_counter = primer_counter - 1
 
             # if primer counter goes below zero, break
             if primer_counter < 0:
                 break
 
     if all_matched:
         amplicon_start = 0