get_pcr_product.py: allow 1 mismatch when evaluating primer amplification

[Paul Villanueva]

This SO answer should be informative, but I would like to avoid using BioPython to limit dependencies.

Also, while we're doing this, see about refactoring the lines below so that it uses a single re.finditer expression instead of two:

MetaFunPrimer/src/get_pcr_product.py

Lines 66 to 86 in f1f6438

 for x in fpri:  # x is the key of the dict fpri, x is the sequence 
     ma = [m.start() for m in re.finditer(x, se)]         
     if len(ma) > 0: 
         for st in ma: 
             tempseq = se[st:] 
             for y in rpri: 
                 rma = [m.start() for m in re.finditer(y, tempseq)] 
                 if len(rma) > 0: 
                     # build an array based on x's forward primer cluster ID, [c001, c002, ...] 
                     fpri_li = fpri[x].split(",") 
                     for i, ff in enumerate(fpri_li): 
                         f = ff.split(".")[-2] 
                         fpri_li[i] = f 
                         #print(fpri_li) 
                                              
                     # build an array based on y's reverse primer cluster ID, [c001, c002, ...] 
                     rpri_li = rpri[y].split(",") 
                     for j, rr in enumerate(rpri_li): 
                         r = rr.split(".")[-2] 
                         rpri_li[j] = r 
                     #print(rpri_li) 

An example from the ISqPCR code I wrote for another app:

    import re
    forward_primer = replace_ambiguous_bases(forward_primer)
    reverse_primer = reverse_complement(replace_ambiguous_bases(reverse_primer))
    primer_pattern = re.compile('({}).*({})'.format(forward_primer, reverse_primer))
    # for match in [match for match in re.finditer(primer_pattern, target_sequence)]:
    for match in re.finditer(primer_pattern, target_sequence):
        product = target_sequence[match.start():match.end()]
        return '{}\t{}\t{}\t{}\t{}\t{}\n'.format(primer_name, target_name, match.start(), match.end(),
                                                 match.end() - match.start(), product)