[Biopython-dev] 8/25 biopython Questions - BioStar

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// Restriction for automated primer design
// August 24, 2010 at 12:39 PM

http://biostar.stackexchange.com/questions/2239/restriction-for-automated-primer-design
Hi,
I am pretty new to BioPython, but I am trying to write a script that would allow the user to input a fasta-file and the multiple cloning site of the target vector. In my script e.g. pQCXIN is the MCS of a vector. I successfully feed digest the insert and get a list of enzymes that does not cut the insert. However, the list lost the order of the restriction sites defined in the beginning of my code (probably because dictionaries are not ordered??). But the order is essential for my primer design step, as I would obviously like to add a 5' RE to my 5' primer...
so basically, how do I get the "no_cutter" as a list that has the same order as the input in the beginning of my code
Any help, suggestions would be appreciated
This is my code so far...

from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Restriction import *
from Bio import SeqIO

##Define the MCS of several vectors this list will get populated while in use##
pQCXIN = RestrictionBatch([NotI,AgeI,BsiWI,PacI,BamHI,EcoRI])
pUC19 = RestrictionBatch([HindIII,SphI,PstI,SalI,XbaI,BamHI,SmaI,KpnI,SacI,EcoRI])

##prompt for vector and insert##
sequence=raw_input('''select your sequence file in FASTA format: ''')
vector=raw_input('''select your vector: ''')
#print vector


for seq in SeqIO.parse(sequence, "fasta"):
    Digest = Analysis(eval(vector), seq.seq, linear=True)
    print seq.id
    #Digest.print_as('map')
    #print Digest.print_that()
    no_cutters = list(Digest.without_site())
    print no_cutters[1].site


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