1 files changed, 65 insertions, 65 deletions
diff --git a/examples/partial_gene_match.py b/examples/partial_gene_match.py
index 8bf5f7c..e19cf8b 100644
--- a/examples/partial_gene_match.py
+++ b/examples/partial_gene_match.py
@@ -1,6 +1,6 @@
 # parital_gene_match.py
 #
-#  Example showing how to create a customized pyparsing Token, in this case, 
+#  Example showing how to create a customized pyparsing Token, in this case,
 #  one that is very much like Literal, but which tolerates up to 'n' character
 #  mismatches
 from pyparsing import *
@@ -12,77 +12,77 @@ datafile = urllib.request.urlopen("http://toxodb.org/common/downloads/release-6.
 fastasrc = datafile.read()
 datafile.close()
 
-""" 
-Sample header: 
+"""
+Sample header:
 >NC_001799-6-2978-2778 | organism=Toxoplasma_gondii_RH | location=NC_001799:2778-2978(-) | length=201
-""" 
-integer = Word(nums).setParseAction(lambda t:int(t[0])) 
-genebit = Group(">" + Word(alphanums.upper()+"-_") + "|" + 
-                Word(printables)("id") + SkipTo("length=", include=True) +  
-                integer("genelen") + LineEnd() +  
-                Combine(OneOrMore(Word("ACGTN")),adjacent=False)("gene")) 
- 
+"""
+integer = Word(nums).setParseAction(lambda t:int(t[0]))
+genebit = Group(">" + Word(alphanums.upper()+"-_") + "|" +
+                Word(printables)("id") + SkipTo("length=", include=True) +
+                integer("genelen") + LineEnd() +
+                Combine(OneOrMore(Word("ACGTN")),adjacent=False)("gene"))
+
 # read gene data from .fasta file - takes just a few seconds
-genedata = OneOrMore(genebit).parseString(fastasrc) 
+genedata = OneOrMore(genebit).parseString(fastasrc)
 
 
-class CloseMatch(Token): 
+class CloseMatch(Token):
     """A special subclass of Token that does *close* matches. For each
        close match of the given string, a tuple is returned giving the
        found close match, and a list of mismatch positions."""
-    def __init__(self, seq, maxMismatches=1): 
-        super(CloseMatch,self).__init__() 
-        self.name = seq 
-        self.sequence = seq 
-        self.maxMismatches = maxMismatches 
-        self.errmsg = "Expected " + self.sequence 
-        self.mayIndexError = False 
-        self.mayReturnEmpty = False 
- 
-    def parseImpl( self, instring, loc, doActions=True ): 
-        start = loc 
-        instrlen = len(instring) 
-        maxloc = start + len(self.sequence) 
- 
-        if maxloc <= instrlen: 
-            seq = self.sequence 
-            seqloc = 0 
-            mismatches = [] 
-            throwException = False 
-            done = False 
-            while loc < maxloc and not done: 
-                if instring[loc] != seq[seqloc]: 
-                    mismatches.append(seqloc) 
-                    if len(mismatches) > self.maxMismatches: 
-                        throwException = True 
-                        done = True 
-                loc += 1 
-                seqloc += 1 
-        else: 
-            throwException = True 
- 
-        if throwException: 
-            exc = self.myException 
-            exc.loc = loc 
-            exc.pstr = instring 
-            raise exc 
- 
-        return loc, (instring[start:loc],mismatches) 
+    def __init__(self, seq, maxMismatches=1):
+        super(CloseMatch,self).__init__()
+        self.name = seq
+        self.sequence = seq
+        self.maxMismatches = maxMismatches
+        self.errmsg = "Expected " + self.sequence
+        self.mayIndexError = False
+        self.mayReturnEmpty = False
+
+    def parseImpl( self, instring, loc, doActions=True ):
+        start = loc
+        instrlen = len(instring)
+        maxloc = start + len(self.sequence)
+
+        if maxloc <= instrlen:
+            seq = self.sequence
+            seqloc = 0
+            mismatches = []
+            throwException = False
+            done = False
+            while loc < maxloc and not done:
+                if instring[loc] != seq[seqloc]:
+                    mismatches.append(seqloc)
+                    if len(mismatches) > self.maxMismatches:
+                        throwException = True
+                        done = True
+                loc += 1
+                seqloc += 1
+        else:
+            throwException = True
+
+        if throwException:
+            exc = self.myException
+            exc.loc = loc
+            exc.pstr = instring
+            raise exc
+
+        return loc, (instring[start:loc],mismatches)
 
 # using the genedata extracted above, look for close matches of a gene sequence
 searchseq = CloseMatch("TTAAATCTAGAAGAT", 3)
-for g in genedata: 
-    print("%s (%d)" % (g.id, g.genelen)) 
-    print("-"*24) 
-    for t,startLoc,endLoc in searchseq.scanString(g.gene, overlap=True): 
-        matched, mismatches = t[0] 
-        print("MATCH:", searchseq.sequence) 
-        print("FOUND:", matched) 
-        if mismatches: 
-            print("      ", ''.join(' ' if i not in mismatches else '*'  
-                            for i,c in enumerate(searchseq.sequence))) 
-        else: 
-            print("<exact match>") 
-        print("at location", startLoc) 
-        print() 
-    print() 
-\ No newline at end of file
+for g in genedata:
+    print("%s (%d)" % (g.id, g.genelen))
+    print("-"*24)
+    for t,startLoc,endLoc in searchseq.scanString(g.gene, overlap=True):
+        matched, mismatches = t[0]
+        print("MATCH:", searchseq.sequence)
+        print("FOUND:", matched)
+        if mismatches:
+            print("      ", ''.join(' ' if i not in mismatches else '*'
+                            for i,c in enumerate(searchseq.sequence)))
+        else:
+            print("<exact match>")
+        print("at location", startLoc)
+        print()
+    print()