Find RE site from AA sequence by Python program

# -*- coding: utf-8 -*-

#/usr/bin/python

"""

Created on Sat Sep 12 12:47:04 2015

@author: Gembu Maryu

"""

import itertools, random

amino = {'A': ['GCC', 'GCT', 'GCG', 'GCA'], 'C': ['TGC', 'TGT'], 'E': ['GAA', 'GAG'], 'D': ['GAC', 'GAT'], 'G': ['GGC', 'GGG', 'GGT', 'GGA'], 'F': ['TTC', 'TTT'], 'I': ['ATA', 'ATC', 'ATT'], 'H': ['CAT', 'CAC'], 'K': ['AAA', 'AAG'], 'M': ['ATG'], 'L': ['CTT', 'TTG', 'CTG', 'TTA', 'CTC','CTA'], 'N': ['AAC', 'AAT'], 'Q': ['CAA', 'CAG'], 'P': ['CCT', 'CCC', 'CCG', 'CCA'], 'S': ['TCT', 'TCC', 'TCG', 'TCA', 'AGC', 'AGT'], 'R': ['AGG', 'CGG', 'CGC', 'CGA', 'AGA', 'CGT'], 'T': ['ACC', 'ACG', 'ACT', 'ACA'], 'W': ['TGG'], 'V': ['GTC','GTT','GTA','GTG'], 'Y': ['TAT','TAC']}

usage = {'A': {1.0: 'GCC', 0.6: 'GCT', 0.1: 'GCG', 0.33: 'GCA'}, 'C': {1.0: 'TGC', 0.46: 'TGT'}, 'E': {0.42: 'GAA', 1.0: 'GAG'}, 'D': {1.0: 'GAC', 0.46: 'GAT'}, 'G': {1.0: 'GGC', 0.66: 'GGG', 0.16: 'GGT', 0.41: 'GGA'}, 'F': {1.0: 'TTC', 0.46: 'TTT'}, 'I': {0.17: 'ATA', 1.0: 'ATC', 0.53: 'ATT'}, 'H': {0.42: 'CAT', 1.0: 'CAC'}, 'K': {0.43: 'AAA', 1.0: 'AAG'}, 'M': {1.0: 'ATG'}, 'L': {0.27: 'CTT', 0.4: 'TTG', 1.0: 'CTG', 0.14: 'TTA', 0.6: 'CTC', 0.06: 'CTA'}, 'N': {1.0: 'AAC', 0.47: 'AAT'}, 'Q': {0.27: 'CAA', 1.0: 'CAG'}, 'P': {0.68: 'CCT', 1.0: 'CCC', 0.11: 'CCG', 0.39: 'CCA'}, 'S': {0.54: 'TCT', 0.76: 'TCC', 0.05: 'TCG', 0.2: 'TCA', 1.0: 'AGC', 0.35: 'AGT'}, 'R': {0.79: 'AGG', 0.58: 'CGG', 0.38: 'CGC', 0.2: 'CGA', 1.0: 'AGA', 0.08: 'CGT'}, 'T': {1.0: 'ACC', 0.11: 'ACG', 0.36: 'ACT', 0.64: 'ACA'}, 'W': {1.0: 'TGG'}, 'V': {0.54: 'GTC', 0.3: 'GTT', 0.12: 'GTA', 1.0: 'GTG'}, 'Y': {1.0: 'TAT', 0.56: 'TAC'}}

res_enz = {'AatII':'gacgtc', 'Asp718':'ggtacc', 'BamHI':'ggatcc', 'BglII':'agatct','ClaI':'atcgat', 'EcoRV':'gatatc','HindIII':'aggcct', 'MluI':'acgcgt', 'PinAI':'ctgcag','PspOMI':'gggccc','PstI':'ctgcag','PviI':'cgatcg','PvuII':'cagctg','SpeI':'actagt','XmaI':'cccggg'}

res_inv = {v:k for k, v in res_enz.items()}

aa_seq = raw_input('Input the amino acid sequence >> ') # wait user input

#aa_seq = 'HSFQKQQREKTRWDNSGRGDE' # sample amino acid sequece

aa_li = [aa_seq[f:f+3] for f in range(len(aa_seq)-2)] # make a list every 3 amino acid

def amino2dna(seq):

genome = ''

seq_list = list(seq)

rand_list = []

for char in seq_list:

        #generate random number(0<rand<1)

rand = random.random()

        rand_list.append(rand)

        #    print rand

cumlo = sorted(usage[char].keys())

comp = 0 #number in cumlo

while comp < len(cumlo):

if rand < cumlo[0]: # compare values

                #            print amino[char][cumlo[0]]

genome = genome + usage[char][cumlo[0]]

                break

elif rand > cumlo[comp] and rand < cumlo[comp+1]:

                #            print amino[char][cumlo[comp+1]]

genome = genome + usage[char][cumlo[comp+1]]

                break

comp = comp + 1

return genome

# make all dna sequence patern from amino acid sequence

for aa_tri in aa_li: # aa_tri: amino acid trio

    #aa_tri = aa_li[1]

dna_seq_list = [' ']

for aa in aa_tri: # aa: single amino acid

codon_list = amino[aa]

        #print codon_list

conn_codon = list(itertools.product(dna_seq_list, codon_list)) # make all dna sequence patern from amino acid sequence

dna_seq_list = [] # reset dna_seq_lit

for tmp in conn_codon:

            dna_seq_list.append(tmp[0]+tmp[1]) # assign a connected dna sequence as valible

        #print dna_seq_list

    # searching presence of restriction enzyme recognition site

for r in res_inv:

for d in dna_seq_list:

if r in d.lower():

print res_inv[r] + ': ' + aa_tri + '('+ d +' )'

aa_split = aa_seq.split(aa_tri)

print aa_split

print amino2dna(aa_split[0]).strip() + d.strip() + amino2dna(aa_split[1]).strip()