198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git python/lib/ucscGb/gbData/ra/raStanza.py python/lib/ucscGb/gbData/ra/raStanza.py
index ec2cbb200c2..900b2da0968 100644
--- python/lib/ucscGb/gbData/ra/raStanza.py
+++ python/lib/ucscGb/gbData/ra/raStanza.py
@@ -1,163 +1,163 @@
 import sys, string
 import re
 from ucscGb.gbData.ordereddict import OrderedDict
 import collections
 
 class RaStanza(OrderedDict):
     '''
     Holds an individual entry in the RaFile.
     '''
 
     @property
     def name(self):
         return self._name
 
     def __init__(self, key=None, value=None):
         OrderedDict.__init__(self)
         if key != None and value != None:
             self[key] = value
             self._name = value
             self._nametype = key
         else:
             self._name = ''
             self._nametype = ''
         
 
     def checkIndent(self, stanza):
         indent = -1
         #print stanza
         for line in stanza:
             i = 0
             while True:
                 #print line[i] + ', ' + str(i) + ', ' + str(indent)
                 if line[i] != ' ':
                     break
                 i = i + 1
             if indent == -1:
                 indent = i / 3
             elif indent != i / 3:
                 raise KeyError('inconsistent indentation')
         if indent == -1:
             raise KeyError('blank stanza')
         #print 'indent = ' + str(indent)
         return indent
         
     def readStanza(self, stanza, key=None, scopes=None):
         '''
         Populates this entry from a single stanza. Override this to create
         custom behavior in derived classes
         '''
         #print stanza
         for line in stanza:
             self.readLine(line)
             
         if scopes != None:
             i = self.checkIndent(stanza)
             
-            if len(scopes) == i: # if we havent hit a scope this low yet, append it
+            if len(scopes) == i: # if we haven't hit a scope this low yet, append it
                 scopes.append(self)
             else: # otherwise we should just set it
                 scopes[i] = self
                 
             if i > 0:
                 self.parent = scopes[i - 1]
                 for pk in self.parent.keys():
                     if pk not in self.keys():
                         self[pk] = self.parent[pk]
 
         return self.readName(stanza, key)
 
 
     def readName(self, stanza, key=None):
         '''
         Extracts the Stanza's name from the value of the first line of the
         stanza.
         '''
         
         if key == None:
             line = stanza[0].strip()
         else:
             line = None
             for s in stanza:
                 if s.split(' ', 1)[0] == key:
                     line = s
                     break
             if line == None:
                 return None
         
         if len(line.split(' ', 1)) != 2:
             raise ValueError()
 
         names = map(str.strip, line.split(' ', 1))
         self._nametype = names[0]
         self._name = names[1]
         #print names
         return names
 
     def readLine(self, line):
         '''
         Reads a single line from the stanza, extracting the key-value pair
         '''
 
         if line.startswith('#') or line == '':
             OrderedDict.append(self, line)
         else:
             raKey = line.split(' ', 1)[0].strip()
             raVal = ''
             if (len(line.split(' ', 1)) == 2):
                 raVal = line.split(' ', 1)[1].strip()
             #if raKey in self:
                 #raise KeyError(raKey + ' already exists')
             self[raKey] = raVal
 
     def difference(self, other):
         '''
         Complement function to summaryDiff.
         Takes in self and a comparison Stanza.
         Returns new stanza with terms from 'self' that are different from 'other'
         Like the summaryDiff, to get the other terms, this needs to be run
         again with self and other switched.
         '''
         retRa = RaStanza()
         retRa._name = self.name
         for key in other.keys():
             try:
                 if other[key] != self[key] and not key.startswith('#'):
                     retRa[key] = self[key]
             except KeyError:
                 continue
                 #maybe add empty keys
         return retRa
 
     def iterkeys(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield item
 
 
     def itervalues(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield self[item]
 
 
     def iteritems(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield item, self[item]
 
 
     def iter(self):
         iterkeys(self)
 
         
     def __str__(self):
         str = ''
         for key in self:
             if key.startswith('#'):
                 str += key + '\n'
             else:
                 str += key + ' ' + self[key] + '\n'
 
         return str