nt_search_regex.py

import re
import Bio.Data.IUPACData

sequence = "GCATGCATCTATACGTAGCTATACTACGATCTACGATCGATCGATGCTATGCATCATGACTACTATGCATCATAGCTGCAT"

pattern = "TATACGTAGCTATACTN{0,100}ATCTACGATCGATCGATGCN{0,100}ACTACTATGCATCATAG"

def nt_search_regex(seq, subseq): 
    """Search for a DNA subseq in sequence. 
    
    use ambiguous values (like N = A or T or C or G, R = A or G etc.) 
    searches only on forward strand 
    """ 
    pattern = '' 
    for nt in subseq:
        if nt in Bio.Data.IUPACData.ambiguous_dna_values.keys():
            value = Bio.Data.IUPACData.ambiguous_dna_values[nt]
        else:
            value = nt
        if len(value) == 1: 
            pattern += value 
        else: 
            pattern += '[%s]' % value 

    pos = -1 
    result = [pattern] 
    l = len(seq) 
    while True: 
        pos += 1 
        s = seq[pos:]
        m = re.search(pattern, s) 
        if not m: 
            break 
        pos += int(m.start(0)) 
        result.append(pos) 
    return result