Iterate over restriction enzymes, finding those with 3' overhang and no ambiguous cut sites

check_enzymes.py

import pdb
from Bio import SeqIO
from Bio import Restriction

seq =  SeqIO.read(open('araTha9/chr5.fas','rU'),'fasta')

for attr,value in Restriction.__dict__.iteritems():
    if not attr.startswith('_'):
        if attr not in ['Restriction', 'RestrictionBatch', 
            'Restriction_Dictionary', 'AllEnzymes', 'Analysis', 'CommOnly', 
            'NonComm','FormattedSeq', 'RanaConfig', 'PrintFormat']:
            #pdb.set_trace()
            # find out if it gives overhang
            if value.is_3overhang():
                if value.ovhg >= 3:
                    # find out how long it is
                    l = len(value.site)
                    # ensure seq. is only A,C,G,T - no monkey business
                    if set(value.site).issubset(set(['A','C','G','T'])):
                        sites = value.search(seq.seq)
                        print attr, l, len(sites), len(sites)/float(len(seq))