from pyparsing import *

import urllib

# read in a bunch of genomic data
datafile = urllib.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): 
        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 