1 files changed, 0 insertions, 88 deletions
diff --git a/trunk/src/examples/partial_gene_match.py b/trunk/src/examples/partial_gene_match.py
deleted file mode 100644
index 8bf5f7c..0000000
--- a/trunk/src/examples/partial_gene_match.py
+++ /dev/null
@@ -1,88 +0,0 @@
-# parital_gene_match.py
-#
-#  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 *
-
-import urllib.request, urllib.parse, urllib.error
-
-# read in a bunch of genomic data
-datafile = urllib.request.urlopen("http://toxodb.org/common/downloads/release-6.0/Tgondii/TgondiiApicoplastORFsNAs_ToxoDB-6.0.fasta")
-fastasrc = datafile.read()
-datafile.close()
-
-""" 
-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")) 
- 
-# read gene data from .fasta file - takes just a few seconds
-genedata = OneOrMore(genebit).parseString(fastasrc) 
-
-
-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) 
-
-# 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